{"text_format":"3","workbook":"xlsx","n_sheets":10,"sheets":["Up in E1 (E1xM1)","Up in M1 (E1xM1)","Up in E2 (E2xM2)","Up in M2 (E2xM2)","Up in E3DO (E3DOxM3)","Up in M3 (E3DOxM3)","Up in E3SU (E3SUxM3)","Up in M3 (E3SUxM3)","Up in E4 (E4xM4)","Up in M4 (E4xM4)"],"not_rendered":{"external_links":2,"defined_names":7},"read":"whole","date_system":"1900"}

{"sheet":"Up in E1 (E1xM1)","index":0,"n_rows":69,"n_cols":15,"rows_kept":69,"merged":[[3,2,3,6],[3,7,3,10],[37,2,37,6],[37,7,37,10]]}
["Additional file 2: Differentially expressed transcripts (DETs) in embryos and megagametophytes at different stages of seed development. "]
["The Arabidopsis genes showing the highest sequence similarity to the Scots pine transcript are presented (#N/A = no alignment to genes in the TAIR database. Cut off value 1e-5)"]
["The highest up-regulated transcripts in E1/M1. Samples subjected to pairwise comparison are highlighted in bold"]
[null,null,"RPKM Embryos ",{"$nulls":4},"RPKM Megagametophytes ",{"$nulls":5},"Arabidopsis homologous gene names and annotation"]
["Transcript ID","Fold change","E1","E2","E3DO","E3SU","E4","M1","M2","M3","M4","At locus ID","At name","At annotation","Involved in"]
["isotig42299",{"v":9.97421329990449,"d":"9.97"},{"$f":"VLOOKUP(A6,'[1]all genes'!$A:$K,3,FALSE)","v":344.004},{"$f":"VLOOKUP(A6,'[1]all genes'!$A:$K,4,FALSE)","v":82.784},{"$f":"VLOOKUP(A6,'[1]all genes'!$A:$K,5,FALSE)","v":93.16},{"$f":"VLOOKUP(A6,'[1]all genes'!$A:$K,6,FALSE)","v":206.886},{"$f":"VLOOKUP(A6,'[1]all genes'!$A:$K,7,FALSE)","v":7.429},{"$f":"VLOOKUP(A6,'[1]all genes'!$A:$K,8,FALSE)","v":0.342},{"$f":"VLOOKUP(A6,'[1]all genes'!$A:$K,9,FALSE)","v":0},{"$f":"VLOOKUP(A6,'[1]all genes'!$A:$K,10,FALSE)","v":0.653},{"$f":"VLOOKUP(A6,'[1]all genes'!$A:$K,11,FALSE)","v":0.734},"No hits"]
["isotig101972",{"v":9.73067847254285,"d":"9.73"},{"$f":"VLOOKUP(A7,'[1]all genes'!$A:$K,3,FALSE)","v":2337.312},{"$f":"VLOOKUP(A7,'[1]all genes'!$A:$K,4,FALSE)","v":1557.12},{"$f":"VLOOKUP(A7,'[1]all genes'!$A:$K,5,FALSE)","v":774.994},{"$f":"VLOOKUP(A7,'[1]all genes'!$A:$K,6,FALSE)","v":1080.524},{"$f":"VLOOKUP(A7,'[1]all genes'!$A:$K,7,FALSE)","v":331.704},{"$f":"VLOOKUP(A7,'[1]all genes'!$A:$K,8,FALSE)","v":2.751},{"$f":"VLOOKUP(A7,'[1]all genes'!$A:$K,9,FALSE)","v":0},{"$f":"VLOOKUP(A7,'[1]all genes'!$A:$K,10,FALSE)","v":0},{"$f":"VLOOKUP(A7,'[1]all genes'!$A:$K,11,FALSE)","v":1.477},"No hits"]
["isotig56640",{"v":8.95973031481398,"d":"8.96"},{"$f":"VLOOKUP(A8,'[1]all genes'!$A:$K,3,FALSE)","v":366.459},{"$f":"VLOOKUP(A8,'[1]all genes'!$A:$K,4,FALSE)","v":151.191},{"$f":"VLOOKUP(A8,'[1]all genes'!$A:$K,5,FALSE)","v":102.056},{"$f":"VLOOKUP(A8,'[1]all genes'!$A:$K,6,FALSE)","v":132.601},{"$f":"VLOOKUP(A8,'[1]all genes'!$A:$K,7,FALSE)","v":21.066},{"$f":"VLOOKUP(A8,'[1]all genes'!$A:$K,8,FALSE)","v":0.736},{"$f":"VLOOKUP(A8,'[1]all genes'!$A:$K,9,FALSE)","v":0.459},{"$f":"VLOOKUP(A8,'[1]all genes'!$A:$K,10,FALSE)","v":0.469},{"$f":"VLOOKUP(A8,'[1]all genes'!$A:$K,11,FALSE)","v":0.527},"No hits"]
["isotig56593",{"v":7.59551179793603,"d":"7.60"},{"$f":"VLOOKUP(A9,'[1]all genes'!$A:$K,3,FALSE)","v":187.22},{"$f":"VLOOKUP(A9,'[1]all genes'!$A:$K,4,FALSE)","v":137.64},{"$f":"VLOOKUP(A9,'[1]all genes'!$A:$K,5,FALSE)","v":88.341},{"$f":"VLOOKUP(A9,'[1]all genes'!$A:$K,6,FALSE)","v":130.891},{"$f":"VLOOKUP(A9,'[1]all genes'!$A:$K,7,FALSE)","v":36.077},{"$f":"VLOOKUP(A9,'[1]all genes'!$A:$K,8,FALSE)","v":0.968},{"$f":"VLOOKUP(A9,'[1]all genes'!$A:$K,9,FALSE)","v":0.907},{"$f":"VLOOKUP(A9,'[1]all genes'!$A:$K,10,FALSE)","v":1.388},{"$f":"VLOOKUP(A9,'[1]all genes'!$A:$K,11,FALSE)","v":1.56},"No hits"]
["isotig39291",{"v":7.17706550112936,"d":"7.18"},{"$f":"VLOOKUP(A10,'[1]all genes'!$A:$K,3,FALSE)","v":209.836},{"$f":"VLOOKUP(A10,'[1]all genes'!$A:$K,4,FALSE)","v":16.905},{"$f":"VLOOKUP(A10,'[1]all genes'!$A:$K,5,FALSE)","v":48.413},{"$f":"VLOOKUP(A10,'[1]all genes'!$A:$K,6,FALSE)","v":0.699},{"$f":"VLOOKUP(A10,'[1]all genes'!$A:$K,7,FALSE)","v":3.752},{"$f":"VLOOKUP(A10,'[1]all genes'!$A:$K,8,FALSE)","v":1.45},{"$f":"VLOOKUP(A10,'[1]all genes'!$A:$K,9,FALSE)","v":0.679},{"$f":"VLOOKUP(A10,'[1]all genes'!$A:$K,10,FALSE)","v":1.386},{"$f":"VLOOKUP(A10,'[1]all genes'!$A:$K,11,FALSE)","v":0.779},"AT4G26880.1",null,"Stigma-specific STIG1-like protein 1 ","unknown"]
["isotig11848",{"v":7.16645344763625,"d":"7.17"},{"$f":"VLOOKUP(A11,'[1]all genes'!$A:$K,3,FALSE)","v":1043.502},{"$f":"VLOOKUP(A11,'[1]all genes'!$A:$K,4,FALSE)","v":656.052},{"$f":"VLOOKUP(A11,'[1]all genes'!$A:$K,5,FALSE)","v":442.745},{"$f":"VLOOKUP(A11,'[1]all genes'!$A:$K,6,FALSE)","v":666.113},{"$f":"VLOOKUP(A11,'[1]all genes'!$A:$K,7,FALSE)","v":166.769},{"$f":"VLOOKUP(A11,'[1]all genes'!$A:$K,8,FALSE)","v":7.264},{"$f":"VLOOKUP(A11,'[1]all genes'!$A:$K,9,FALSE)","v":5.565},{"$f":"VLOOKUP(A11,'[1]all genes'!$A:$K,10,FALSE)","v":4.417},{"$f":"VLOOKUP(A11,'[1]all genes'!$A:$K,11,FALSE)","v":5.319},"No hits"]
["isotig38581",{"v":7.15119779337341,"d":"7.15"},{"$f":"VLOOKUP(A12,'[1]all genes'!$A:$K,3,FALSE)","v":53.73},{"$f":"VLOOKUP(A12,'[1]all genes'!$A:$K,4,FALSE)","v":113.592},{"$f":"VLOOKUP(A12,'[1]all genes'!$A:$K,5,FALSE)","v":69.151},{"$f":"VLOOKUP(A12,'[1]all genes'!$A:$K,6,FALSE)","v":214.241},{"$f":"VLOOKUP(A12,'[1]all genes'!$A:$K,7,FALSE)","v":43.036},{"$f":"VLOOKUP(A12,'[1]all genes'!$A:$K,8,FALSE)","v":0.378},{"$f":"VLOOKUP(A12,'[1]all genes'!$A:$K,9,FALSE)","v":0.354},{"$f":"VLOOKUP(A12,'[1]all genes'!$A:$K,10,FALSE)","v":0.722},{"$f":"VLOOKUP(A12,'[1]all genes'!$A:$K,11,FALSE)","v":2.03},"AT5G09970.1","CYP78A7","Cytochrome P450 78A7 ","regulation of growth"]
["isotig62881",{"v":7.05723718673327,"d":"7.06"},{"$f":"VLOOKUP(A13,'[1]all genes'!$A:$K,3,FALSE)","v":129.984},{"$f":"VLOOKUP(A13,'[1]all genes'!$A:$K,4,FALSE)","v":0.632},{"$f":"VLOOKUP(A13,'[1]all genes'!$A:$K,5,FALSE)","v":0},{"$f":"VLOOKUP(A13,'[1]all genes'!$A:$K,6,FALSE)","v":0},{"$f":"VLOOKUP(A13,'[1]all genes'!$A:$K,7,FALSE)","v":0.505},{"$f":"VLOOKUP(A13,'[1]all genes'!$A:$K,8,FALSE)","v":0.976},{"$f":"VLOOKUP(A13,'[1]all genes'!$A:$K,9,FALSE)","v":0},{"$f":"VLOOKUP(A13,'[1]all genes'!$A:$K,10,FALSE)","v":0},{"$f":"VLOOKUP(A13,'[1]all genes'!$A:$K,11,FALSE)","v":0},"AT5G53190.1","SWEET3","Bidirectional sugar transporter SWEET3 ","carbohydrate transmembrane transport"]
["isotig61160",{"v":7.02919882924505,"d":"7.03"},{"$f":"VLOOKUP(A14,'[1]all genes'!$A:$K,3,FALSE)","v":112.2},{"$f":"VLOOKUP(A14,'[1]all genes'!$A:$K,4,FALSE)","v":5.563},{"$f":"VLOOKUP(A14,'[1]all genes'!$A:$K,5,FALSE)","v":3.929},{"$f":"VLOOKUP(A14,'[1]all genes'!$A:$K,6,FALSE)","v":0},{"$f":"VLOOKUP(A14,'[1]all genes'!$A:$K,7,FALSE)","v":0.889},{"$f":"VLOOKUP(A14,'[1]all genes'!$A:$K,8,FALSE)","v":0.859},{"$f":"VLOOKUP(A14,'[1]all genes'!$A:$K,9,FALSE)","v":0},{"$f":"VLOOKUP(A14,'[1]all genes'!$A:$K,10,FALSE)","v":0.41},{"$f":"VLOOKUP(A14,'[1]all genes'!$A:$K,11,FALSE)","v":0},"AT1G22380.1","UGT85A3","UDP-glycosyltransferase 85A3 ","transferase activity"]
["isotig40165",{"v":6.84919971781579,"d":"6.85"},{"$f":"VLOOKUP(A15,'[1]all genes'!$A:$K,3,FALSE)","v":768.679},{"$f":"VLOOKUP(A15,'[1]all genes'!$A:$K,4,FALSE)","v":486.064},{"$f":"VLOOKUP(A15,'[1]all genes'!$A:$K,5,FALSE)","v":306.871},{"$f":"VLOOKUP(A15,'[1]all genes'!$A:$K,6,FALSE)","v":402.103},{"$f":"VLOOKUP(A15,'[1]all genes'!$A:$K,7,FALSE)","v":158.957},{"$f":"VLOOKUP(A15,'[1]all genes'!$A:$K,8,FALSE)","v":6.667},{"$f":"VLOOKUP(A15,'[1]all genes'!$A:$K,9,FALSE)","v":3.344},{"$f":"VLOOKUP(A15,'[1]all genes'!$A:$K,10,FALSE)","v":5.916},{"$f":"VLOOKUP(A15,'[1]all genes'!$A:$K,11,FALSE)","v":7.416},"No hits"]
["isotig50289",{"v":6.84045478487704,"d":"6.84"},{"$f":"VLOOKUP(A16,'[1]all genes'!$A:$K,3,FALSE)","v":170.753},{"$f":"VLOOKUP(A16,'[1]all genes'!$A:$K,4,FALSE)","v":18.333},{"$f":"VLOOKUP(A16,'[1]all genes'!$A:$K,5,FALSE)","v":23.848},{"$f":"VLOOKUP(A16,'[1]all genes'!$A:$K,6,FALSE)","v":0},{"$f":"VLOOKUP(A16,'[1]all genes'!$A:$K,7,FALSE)","v":0.771},{"$f":"VLOOKUP(A16,'[1]all genes'!$A:$K,8,FALSE)","v":1.49},{"$f":"VLOOKUP(A16,'[1]all genes'!$A:$K,9,FALSE)","v":2.092},{"$f":"VLOOKUP(A16,'[1]all genes'!$A:$K,10,FALSE)","v":2.136},{"$f":"VLOOKUP(A16,'[1]all genes'!$A:$K,11,FALSE)","v":1.6},"AT1G02335.1","GL22","Germin-like protein subfamily 2 member 2 ","metal ion binding; nutrient reservoir activity"]
["isotig62762",{"v":6.76376694259904,"d":"6.76"},{"$f":"VLOOKUP(A17,'[1]all genes'!$A:$K,3,FALSE)","v":373.053},{"$f":"VLOOKUP(A17,'[1]all genes'!$A:$K,4,FALSE)","v":22.234},{"$f":"VLOOKUP(A17,'[1]all genes'!$A:$K,5,FALSE)","v":35.888},{"$f":"VLOOKUP(A17,'[1]all genes'!$A:$K,6,FALSE)","v":1.418},{"$f":"VLOOKUP(A17,'[1]all genes'!$A:$K,7,FALSE)","v":5.076},{"$f":"VLOOKUP(A17,'[1]all genes'!$A:$K,8,FALSE)","v":3.433},{"$f":"VLOOKUP(A17,'[1]all genes'!$A:$K,9,FALSE)","v":1.378},{"$f":"VLOOKUP(A17,'[1]all genes'!$A:$K,10,FALSE)","v":0.469},{"$f":"VLOOKUP(A17,'[1]all genes'!$A:$K,11,FALSE)","v":3.16},"AT1G69830.1","AMY3","Alpha-amylase 3, chloroplastic ","carbohydrate metabolic process"]
["isotig65228",{"v":6.71388262116292,"d":"6.71"},{"$f":"VLOOKUP(A18,'[1]all genes'!$A:$K,3,FALSE)","v":59.625},{"$f":"VLOOKUP(A18,'[1]all genes'!$A:$K,4,FALSE)","v":11.768},{"$f":"VLOOKUP(A18,'[1]all genes'!$A:$K,5,FALSE)","v":11.946},{"$f":"VLOOKUP(A18,'[1]all genes'!$A:$K,6,FALSE)","v":0},{"$f":"VLOOKUP(A18,'[1]all genes'!$A:$K,7,FALSE)","v":1.175},{"$f":"VLOOKUP(A18,'[1]all genes'!$A:$K,8,FALSE)","v":0.568},{"$f":"VLOOKUP(A18,'[1]all genes'!$A:$K,9,FALSE)","v":0},{"$f":"VLOOKUP(A18,'[1]all genes'!$A:$K,10,FALSE)","v":0},{"$f":"VLOOKUP(A18,'[1]all genes'!$A:$K,11,FALSE)","v":0},"AT5G55250.1","IAMT1","Indole-3-acetate O-methyltransferase 1 ","auxin homeostasis; polarity specification of adaxial/abaxial axis"]
["isotig69298",{"v":6.66135097129496,"d":"6.66"},{"$f":"VLOOKUP(A19,'[1]all genes'!$A:$K,3,FALSE)","v":71.765},{"$f":"VLOOKUP(A19,'[1]all genes'!$A:$K,4,FALSE)","v":12.864},{"$f":"VLOOKUP(A19,'[1]all genes'!$A:$K,5,FALSE)","v":20.115},{"$f":"VLOOKUP(A19,'[1]all genes'!$A:$K,6,FALSE)","v":0},{"$f":"VLOOKUP(A19,'[1]all genes'!$A:$K,7,FALSE)","v":0.734},{"$f":"VLOOKUP(A19,'[1]all genes'!$A:$K,8,FALSE)","v":0.709},{"$f":"VLOOKUP(A19,'[1]all genes'!$A:$K,9,FALSE)","v":0},{"$f":"VLOOKUP(A19,'[1]all genes'!$A:$K,10,FALSE)","v":0.678},{"$f":"VLOOKUP(A19,'[1]all genes'!$A:$K,11,FALSE)","v":1.524},"AT4G39700.1",null,"Heavy metal transport/detoxification superfamily protein ","metal ion transport"]
["isotig32836",{"v":6.62428563053219,"d":"6.62"},{"$f":"VLOOKUP(A20,'[1]all genes'!$A:$K,3,FALSE)","v":28.116},{"$f":"VLOOKUP(A20,'[1]all genes'!$A:$K,4,FALSE)","v":7.756},{"$f":"VLOOKUP(A20,'[1]all genes'!$A:$K,5,FALSE)","v":6.26},{"$f":"VLOOKUP(A20,'[1]all genes'!$A:$K,6,FALSE)","v":4.947},{"$f":"VLOOKUP(A20,'[1]all genes'!$A:$K,7,FALSE)","v":0.885},{"$f":"VLOOKUP(A20,'[1]all genes'!$A:$K,8,FALSE)","v":0.285},{"$f":"VLOOKUP(A20,'[1]all genes'!$A:$K,9,FALSE)","v":0.267},{"$f":"VLOOKUP(A20,'[1]all genes'!$A:$K,10,FALSE)","v":0},{"$f":"VLOOKUP(A20,'[1]all genes'!$A:$K,11,FALSE)","v":0},"AT3G14240.1",null,"Subtilase family protein ","proteolysis, negative regulation of catalytic activity"]
["isotig60719",{"v":6.48735460806734,"d":"6.49"},{"$f":"VLOOKUP(A21,'[1]all genes'!$A:$K,3,FALSE)","v":37.144},{"$f":"VLOOKUP(A21,'[1]all genes'!$A:$K,4,FALSE)","v":14.492},{"$f":"VLOOKUP(A21,'[1]all genes'!$A:$K,5,FALSE)","v":14.403},{"$f":"VLOOKUP(A21,'[1]all genes'!$A:$K,6,FALSE)","v":19.571},{"$f":"VLOOKUP(A21,'[1]all genes'!$A:$K,7,FALSE)","v":0},{"$f":"VLOOKUP(A21,'[1]all genes'!$A:$K,8,FALSE)","v":0.414},{"$f":"VLOOKUP(A21,'[1]all genes'!$A:$K,9,FALSE)","v":1.552},{"$f":"VLOOKUP(A21,'[1]all genes'!$A:$K,10,FALSE)","v":0.792},{"$f":"VLOOKUP(A21,'[1]all genes'!$A:$K,11,FALSE)","v":0.89},"No hits"]
["isotig101683",{"v":6.48591264883212,"d":"6.49"},{"$f":"VLOOKUP(A22,'[1]all genes'!$A:$K,3,FALSE)","v":121.18},{"$f":"VLOOKUP(A22,'[1]all genes'!$A:$K,4,FALSE)","v":12.257},{"$f":"VLOOKUP(A22,'[1]all genes'!$A:$K,5,FALSE)","v":2.473},{"$f":"VLOOKUP(A22,'[1]all genes'!$A:$K,6,FALSE)","v":5.212},{"$f":"VLOOKUP(A22,'[1]all genes'!$A:$K,7,FALSE)","v":0},{"$f":"VLOOKUP(A22,'[1]all genes'!$A:$K,8,FALSE)","v":1.352},{"$f":"VLOOKUP(A22,'[1]all genes'!$A:$K,9,FALSE)","v":0},{"$f":"VLOOKUP(A22,'[1]all genes'!$A:$K,10,FALSE)","v":0},{"$f":"VLOOKUP(A22,'[1]all genes'!$A:$K,11,FALSE)","v":0},"AT1G75950.1","SKP1A","SKP1-like protein 1A ","auxin-activated signaling pathway"]
["isotig59039",{"v":6.46432327726886,"d":"6.46"},{"$f":"VLOOKUP(A23,'[1]all genes'!$A:$K,3,FALSE)","v":31.611},{"$f":"VLOOKUP(A23,'[1]all genes'!$A:$K,4,FALSE)","v":1.854},{"$f":"VLOOKUP(A23,'[1]all genes'!$A:$K,5,FALSE)","v":1.636},{"$f":"VLOOKUP(A23,'[1]all genes'!$A:$K,6,FALSE)","v":0.345},{"$f":"VLOOKUP(A23,'[1]all genes'!$A:$K,7,FALSE)","v":0.37},{"$f":"VLOOKUP(A23,'[1]all genes'!$A:$K,8,FALSE)","v":0.358},{"$f":"VLOOKUP(A23,'[1]all genes'!$A:$K,9,FALSE)","v":0.335},{"$f":"VLOOKUP(A23,'[1]all genes'!$A:$K,10,FALSE)","v":0.342},{"$f":"VLOOKUP(A23,'[1]all genes'!$A:$K,11,FALSE)","v":0.384},"AT3G61740.1","ATX3","Histone-lysine N-methyltransferase ATX3 "," regulation of transcription, DNA-dependent"]
["isotig59351",{"v":6.36724603939038,"d":"6.37"},{"$f":"VLOOKUP(A24,'[1]all genes'!$A:$K,3,FALSE)","v":60.924},{"$f":"VLOOKUP(A24,'[1]all genes'!$A:$K,4,FALSE)","v":5.255},{"$f":"VLOOKUP(A24,'[1]all genes'!$A:$K,5,FALSE)","v":6.747},{"$f":"VLOOKUP(A24,'[1]all genes'!$A:$K,6,FALSE)","v":0.711},{"$f":"VLOOKUP(A24,'[1]all genes'!$A:$K,7,FALSE)","v":2.29},{"$f":"VLOOKUP(A24,'[1]all genes'!$A:$K,8,FALSE)","v":0.738},{"$f":"VLOOKUP(A24,'[1]all genes'!$A:$K,9,FALSE)","v":0.345},{"$f":"VLOOKUP(A24,'[1]all genes'!$A:$K,10,FALSE)","v":0.352},{"$f":"VLOOKUP(A24,'[1]all genes'!$A:$K,11,FALSE)","v":1.188},"AT3G48080.1","EDS1B","Protein EDS1B "," lipid metabolic process"]
["isotig21539",{"v":6.238429815936,"d":"6.24"},{"$f":"VLOOKUP(A25,'[1]all genes'!$A:$K,3,FALSE)","v":28.766},{"$f":"VLOOKUP(A25,'[1]all genes'!$A:$K,4,FALSE)","v":20.22},{"$f":"VLOOKUP(A25,'[1]all genes'!$A:$K,5,FALSE)","v":22.289},{"$f":"VLOOKUP(A25,'[1]all genes'!$A:$K,6,FALSE)","v":1.468},{"$f":"VLOOKUP(A25,'[1]all genes'!$A:$K,7,FALSE)","v":4.729},{"$f":"VLOOKUP(A25,'[1]all genes'!$A:$K,8,FALSE)","v":0.381},{"$f":"VLOOKUP(A25,'[1]all genes'!$A:$K,9,FALSE)","v":0},{"$f":"VLOOKUP(A25,'[1]all genes'!$A:$K,10,FALSE)","v":0.364},{"$f":"VLOOKUP(A25,'[1]all genes'!$A:$K,11,FALSE)","v":1.227},"AT3G26200.1","CYP71B22","Cytochrome P450 71B22 ","oxidation-reduction process"]
["isotig10972",{"v":6.16326936835054,"d":"6.16"},{"$f":"VLOOKUP(A26,'[1]all genes'!$A:$K,3,FALSE)","v":2341.7},{"$f":"VLOOKUP(A26,'[1]all genes'!$A:$K,4,FALSE)","v":64.944},{"$f":"VLOOKUP(A26,'[1]all genes'!$A:$K,5,FALSE)","v":40.708},{"$f":"VLOOKUP(A26,'[1]all genes'!$A:$K,6,FALSE)","v":4.344},{"$f":"VLOOKUP(A26,'[1]all genes'!$A:$K,7,FALSE)","v":11.079},{"$f":"VLOOKUP(A26,'[1]all genes'!$A:$K,8,FALSE)","v":32.674},{"$f":"VLOOKUP(A26,'[1]all genes'!$A:$K,9,FALSE)","v":20.572},{"$f":"VLOOKUP(A26,'[1]all genes'!$A:$K,10,FALSE)","v":15.074},{"$f":"VLOOKUP(A26,'[1]all genes'!$A:$K,11,FALSE)","v":20.571},"AT2G30870.1","GSTF10","Glutathione S-transferase F10 ","response to toxic substance"]
["isotig51549",{"v":6.13892423000644,"d":"6.14"},{"$f":"VLOOKUP(A27,'[1]all genes'!$A:$K,3,FALSE)","v":54.05},{"$f":"VLOOKUP(A27,'[1]all genes'!$A:$K,4,FALSE)","v":0.994},{"$f":"VLOOKUP(A27,'[1]all genes'!$A:$K,5,FALSE)","v":4.212},{"$f":"VLOOKUP(A27,'[1]all genes'!$A:$K,6,FALSE)","v":0},{"$f":"VLOOKUP(A27,'[1]all genes'!$A:$K,7,FALSE)","v":0},{"$f":"VLOOKUP(A27,'[1]all genes'!$A:$K,8,FALSE)","v":0.767},{"$f":"VLOOKUP(A27,'[1]all genes'!$A:$K,9,FALSE)","v":1.437},{"$f":"VLOOKUP(A27,'[1]all genes'!$A:$K,10,FALSE)","v":0},{"$f":"VLOOKUP(A27,'[1]all genes'!$A:$K,11,FALSE)","v":0.824},"AT1G10370.1","GSTU17","Glutathione S-transferase U17 ","response to growth hormone"]
["isotig82212",{"v":6.00111695657992,"d":"6.00"},{"$f":"VLOOKUP(A28,'[1]all genes'!$A:$K,3,FALSE)","v":59.438},{"$f":"VLOOKUP(A28,'[1]all genes'!$A:$K,4,FALSE)","v":19.239},{"$f":"VLOOKUP(A28,'[1]all genes'!$A:$K,5,FALSE)","v":5.944},{"$f":"VLOOKUP(A28,'[1]all genes'!$A:$K,6,FALSE)","v":8.053},{"$f":"VLOOKUP(A28,'[1]all genes'!$A:$K,7,FALSE)","v":3.843},{"$f":"VLOOKUP(A28,'[1]all genes'!$A:$K,8,FALSE)","v":0.928},{"$f":"VLOOKUP(A28,'[1]all genes'!$A:$K,9,FALSE)","v":0},{"$f":"VLOOKUP(A28,'[1]all genes'!$A:$K,10,FALSE)","v":1.774},{"$f":"VLOOKUP(A28,'[1]all genes'!$A:$K,11,FALSE)","v":1.994},"AT1G47128.1","RD21A","Cysteine proteinase RD21a ","proteolysis involved in cellular protein catabolic process"]
["isotig35313",{"v":6.00035396134191,"d":"6.00"},{"$f":"VLOOKUP(A29,'[1]all genes'!$A:$K,3,FALSE)","v":126.367},{"$f":"VLOOKUP(A29,'[1]all genes'!$A:$K,4,FALSE)","v":21.303},{"$f":"VLOOKUP(A29,'[1]all genes'!$A:$K,5,FALSE)","v":25.273},{"$f":"VLOOKUP(A29,'[1]all genes'!$A:$K,6,FALSE)","v":3.805},{"$f":"VLOOKUP(A29,'[1]all genes'!$A:$K,7,FALSE)","v":9.533},{"$f":"VLOOKUP(A29,'[1]all genes'!$A:$K,8,FALSE)","v":1.974},{"$f":"VLOOKUP(A29,'[1]all genes'!$A:$K,9,FALSE)","v":3.08},{"$f":"VLOOKUP(A29,'[1]all genes'!$A:$K,10,FALSE)","v":1.886},{"$f":"VLOOKUP(A29,'[1]all genes'!$A:$K,11,FALSE)","v":2.12},"No hits"]
["isotig26983",{"v":5.98187940396343,"d":"5.98"},{"$f":"VLOOKUP(A30,'[1]all genes'!$A:$K,3,FALSE)","v":64.718},{"$f":"VLOOKUP(A30,'[1]all genes'!$A:$K,4,FALSE)","v":72.539},{"$f":"VLOOKUP(A30,'[1]all genes'!$A:$K,5,FALSE)","v":40.917},{"$f":"VLOOKUP(A30,'[1]all genes'!$A:$K,6,FALSE)","v":33.573},{"$f":"VLOOKUP(A30,'[1]all genes'!$A:$K,7,FALSE)","v":32.163},{"$f":"VLOOKUP(A30,'[1]all genes'!$A:$K,8,FALSE)","v":1.024},{"$f":"VLOOKUP(A30,'[1]all genes'!$A:$K,9,FALSE)","v":0.639},{"$f":"VLOOKUP(A30,'[1]all genes'!$A:$K,10,FALSE)","v":0},{"$f":"VLOOKUP(A30,'[1]all genes'!$A:$K,11,FALSE)","v":1.1},"AT1G76160.1","sks5","SKU5 similar 5 ","  oxidation reduction"]
["isotig25980",{"v":5.95365768519225,"d":"5.95"},{"$f":"VLOOKUP(A31,'[1]all genes'!$A:$K,3,FALSE)","v":345.459},{"$f":"VLOOKUP(A31,'[1]all genes'!$A:$K,4,FALSE)","v":62.089},{"$f":"VLOOKUP(A31,'[1]all genes'!$A:$K,5,FALSE)","v":59.14},{"$f":"VLOOKUP(A31,'[1]all genes'!$A:$K,6,FALSE)","v":2.149},{"$f":"VLOOKUP(A31,'[1]all genes'!$A:$K,7,FALSE)","v":23.076},{"$f":"VLOOKUP(A31,'[1]all genes'!$A:$K,8,FALSE)","v":5.574},{"$f":"VLOOKUP(A31,'[1]all genes'!$A:$K,9,FALSE)","v":12.525},{"$f":"VLOOKUP(A31,'[1]all genes'!$A:$K,10,FALSE)","v":1.065},{"$f":"VLOOKUP(A31,'[1]all genes'!$A:$K,11,FALSE)","v":8.381},"No hits"]
["isotig18285",{"v":5.94246459286744,"d":"5.94"},{"$f":"VLOOKUP(A32,'[1]all genes'!$A:$K,3,FALSE)","v":14.452},{"$f":"VLOOKUP(A32,'[1]all genes'!$A:$K,4,FALSE)","v":4.568},{"$f":"VLOOKUP(A32,'[1]all genes'!$A:$K,5,FALSE)","v":4.946},{"$f":"VLOOKUP(A32,'[1]all genes'!$A:$K,6,FALSE)","v":1.813},{"$f":"VLOOKUP(A32,'[1]all genes'!$A:$K,7,FALSE)","v":2.434},{"$f":"VLOOKUP(A32,'[1]all genes'!$A:$K,8,FALSE)","v":0.235},{"$f":"VLOOKUP(A32,'[1]all genes'!$A:$K,9,FALSE)","v":0},{"$f":"VLOOKUP(A32,'[1]all genes'!$A:$K,10,FALSE)","v":0},{"$f":"VLOOKUP(A32,'[1]all genes'!$A:$K,11,FALSE)","v":0.758},"AT4G29720.1","PAO5","Probable polyamine oxidase 5 ","regulation of timing of transition from vegetative to reproductive phase"]
["isotig50389",{"v":5.9418510447431,"d":"5.94"},{"$f":"VLOOKUP(A33,'[1]all genes'!$A:$K,3,FALSE)","v":44.567},{"$f":"VLOOKUP(A33,'[1]all genes'!$A:$K,4,FALSE)","v":6.574},{"$f":"VLOOKUP(A33,'[1]all genes'!$A:$K,5,FALSE)","v":1.326},{"$f":"VLOOKUP(A33,'[1]all genes'!$A:$K,6,FALSE)","v":6.29},{"$f":"VLOOKUP(A33,'[1]all genes'!$A:$K,7,FALSE)","v":19.512},{"$f":"VLOOKUP(A33,'[1]all genes'!$A:$K,8,FALSE)","v":0.725},{"$f":"VLOOKUP(A33,'[1]all genes'!$A:$K,9,FALSE)","v":0},{"$f":"VLOOKUP(A33,'[1]all genes'!$A:$K,10,FALSE)","v":0},{"$f":"VLOOKUP(A33,'[1]all genes'!$A:$K,11,FALSE)","v":0},"No hits"]
["isotig63780",{"v":5.93126888756844,"d":"5.93"},{"$f":"VLOOKUP(A34,'[1]all genes'!$A:$K,3,FALSE)","v":95.012},{"$f":"VLOOKUP(A34,'[1]all genes'!$A:$K,4,FALSE)","v":57.797},{"$f":"VLOOKUP(A34,'[1]all genes'!$A:$K,5,FALSE)","v":62.645},{"$f":"VLOOKUP(A34,'[1]all genes'!$A:$K,6,FALSE)","v":5.001},{"$f":"VLOOKUP(A34,'[1]all genes'!$A:$K,7,FALSE)","v":5.37},{"$f":"VLOOKUP(A34,'[1]all genes'!$A:$K,8,FALSE)","v":1.557},{"$f":"VLOOKUP(A34,'[1]all genes'!$A:$K,9,FALSE)","v":3.886},{"$f":"VLOOKUP(A34,'[1]all genes'!$A:$K,10,FALSE)","v":0.496},{"$f":"VLOOKUP(A34,'[1]all genes'!$A:$K,11,FALSE)","v":1.114},"AT5G60530.1","LEA","late embryogenesis abundant protein-related / LEA protein-related ","transition metal ion transport"]
["isotig60425",{"v":5.91271151478219,"d":"5.91"},{"$f":"VLOOKUP(A35,'[1]all genes'!$A:$K,3,FALSE)","v":24.338},{"$f":"VLOOKUP(A35,'[1]all genes'!$A:$K,4,FALSE)","v":2.095},{"$f":"VLOOKUP(A35,'[1]all genes'!$A:$K,5,FALSE)","v":4.808},{"$f":"VLOOKUP(A35,'[1]all genes'!$A:$K,6,FALSE)","v":1.559},{"$f":"VLOOKUP(A35,'[1]all genes'!$A:$K,7,FALSE)","v":1.256},{"$f":"VLOOKUP(A35,'[1]all genes'!$A:$K,8,FALSE)","v":0.404},{"$f":"VLOOKUP(A35,'[1]all genes'!$A:$K,9,FALSE)","v":1.515},{"$f":"VLOOKUP(A35,'[1]all genes'!$A:$K,10,FALSE)","v":0.386},{"$f":"VLOOKUP(A35,'[1]all genes'!$A:$K,11,FALSE)","v":0.434},"AT4G32940.1","GAMMA-VPE","Vacuolar-processing enzyme gamma-isozyme ","response to hormones"]
[]
["The highest up-regulated transcripts in E1 when M1 RPKM value was equal to 0. "]
[null,null,"RPKM Embryos ",{"$nulls":4},"RPKM Megagametophytes ",{"$nulls":5},"Arabidopsis homologous gene names and annotation"]
["Transcript ID","Fold change","E1","E2","E3DO","E3SU","E4","M1","M2","M3","M4","At locus ID","At name","At annotation","Involved in"]
["isotig98833",{"v":99,"d":"99.00"},980.78,494.428,351.408,472.717,153.43,0,0,1.18,0,"AT5G23870.2","PAE9","Pectin acetylesterase 9 ","cell wall loosening"]
["isotig18163",{"v":99,"d":"99.00"},297.588,287.147,411.141,150.315,30.857,0,0,0,0,"AT5G62360.1",null,"Plant invertase/pectin methylesterase inhibitor superfamily protein ","negative regulation of catalytic activity"]
["isotig93401",{"v":99,"d":"99.00"},292.782,72.613,51.277,117.608,7.964,0,0,0,1.181,"AT1G01190.1","CYP78A8","cytochrome P450, family 78, subfamily A, polypeptide 8 ","oxidation-reduction process"]
["isotig14330",{"v":99,"d":"99.00"},234.826,92.652,80.893,23.818,2.019,0,0,0,0,"AT4G38400.1","EXLA2","Expansin-like A2 ","sexual reproduction"]
["isotig71172",{"v":99,"d":"99.00"},208.104,29.647,56.527,19.856,14.214,0,0,0,0,"AT5G67070.1","RALFL34","Protein RALF-like 34 ","cell-cell signaling; hormone activity"]
["isotig04574",{"v":99,"d":"99.00"},203.454,50.966,34.9,56.315,3.394,0,0,0,0,"AT5G09970.1","CYP78A7","Cytochrome P450 78A7 ","regulation of growth"]
["isotig44201",{"v":99,"d":"99.00"},182.288,35.528,72.725,56.892,11.859,0,0,0,0.746,"No hits"]
["isotig25556",{"v":99,"d":"99.00"},170.334,77.394,85.883,112.444,92.764,0,0,0,0,"AT1G10460.1","GLP7","Germin-like protein subfamily 1 member 1 ","manganese ion binding; nutrient reservoir activity"]
["isotig105225",{"v":99,"d":"99.00"},141.863,38.948,21.714,45.764,1.638,0,0,0,0,"AT5G09970.1","CYP78A7","Cytochrome P450 78A7 ","regulation of growth"]
["isotig28522",{"v":99,"d":"99.00"},122.291,9.953,8.032,1.587,1.704,0,0,0,0,"AT1G60710.1","ATB2","Probable aldo-keto reductase 4 ","oxidation-reduction process"]
["isotig27999",{"v":99,"d":"99.00"},117.606,20.636,13.715,0,0,0,0,0,0,"AT4G09610.1","GASA2","Gibberellin-regulated protein 2 ","response to gibberellin stimulus"]
["isotig62250",{"v":99,"d":"99.00"},92.295,13.337,8.134,0.451,3.391,0,0.438,0.894,1.508,"AT1G03230.1",null,"Eukaryotic aspartyl protease family protein ","response to salt stress"]
["isotig113839",{"v":99,"d":"99.00"},90.258,91.296,46.888,24.705,13.264,0,0,6.123,0,"No hits"]
["isotig78926",{"v":99,"d":"99.00"},88.551,87.272,128.934,17.945,13.764,0,1.66,1.694,0.952,"AT5G62360.1",null,"Plant invertase/pectin methylesterase inhibitor superfamily protein ","negative regulation of catalytic activity"]
["isotig98557",{"v":99,"d":"99.00"},88.31,17.546,9.011,0,1.275,0,4.612,3.53,3.968,"No hits"]
["isotig39233",{"v":99,"d":"99.00"},87.537,11.285,23.294,9.044,0.694,0,0,0,0.72,"AT4G38400.1","EXLA2","Expansin-like A2 ","sexual reproduction"]
["isotig19551",{"v":99,"d":"99.00"},84.732,45.71,52.453,39.685,3.044,0,0,0,0,"No hits"]
["isotig77785",{"v":99,"d":"99.00"},75.917,1.129,3.987,0.84,0,0,0,0,0.936,"AT2G23690.1",null,"unknown protein","unknown"]
["isotig28596",{"v":99,"d":"99.00"},75.654,14.653,24.145,1.817,6.505,0,0,0,0,"AT2G36790.1","UGT73C6","UDP-glycosyltransferase 73C6 ","flavonol biosynthetic process"]
["isotig54539",{"v":99,"d":"99.00"},71.987,0,4.114,0,2.327,0,0,0,0,"AT5G57625.1",null,"CAP (Cysteine-rich secretory proteins, Antigen 5, and Pathogenesis-related 1 protein) superfamily protein ","unknown"]
["isotig46869",{"v":99,"d":"99.00"},71.563,3.731,10.539,0.555,5.367,0,0.539,1.652,1.238,"AT1G12600.1","UTR4","UDP-galactose/UDP-glucose transporter 4 ","transmembrane transport"]
["isotig114968",{"v":99,"d":"99.00"},71.409,4.815,34.005,10.75,3.848,0,0,0,0,"No hits"]
["isotig80926",{"v":99,"d":"99.00"},66.97,0,4.196,0,0,0,0,0,0,"AT1G71050.1","HIPP20","Heavy metal transport/detoxification superfamily protein ","metal ion transport"]
["isotig34613",{"v":99,"d":"99.00"},64.723,23.021,19.305,0,2.299,0,0,0,2.386,"AT5G55250.1","IAMT1","Indole-3-acetate O-methyltransferase 1 ","auxin homeostasis; polarity specification of adaxial/abaxial axis"]
["isotig65493",{"v":99,"d":"99.00"},59.107,6.726,3.694,0.556,0,0,1.08,0.551,2.479,"AT5G54160.1","OMT1","Flavone 3'-O-methyltransferase 1 ","flavonol biosynthetic process"]
["isotig80545",{"v":99,"d":"99.00"},58.07,3.524,3.318,0,0,0,0.849,0,0.974,"No hits"]
["isotig28869",{"v":99,"d":"99.00"},57.641,28.602,27.966,34.382,58.016,0,0,0,1.824,"AT5G67070.1","RALFL34","Protein RALF-like 34 ","cell-cell signaling; hormone activity"]
["isotig48941",{"v":99,"d":"99.00"},57.015,1.722,4.255,3.203,0,0,0,0.635,0,"AT1G71830.1","SERK1","Somatic embryogenesis receptor kinase 1 ","embryo development ending in seed dormancy"]
["isotig41809",{"v":99,"d":"99.00"},55.68,208.872,124.012,233.316,19.844,0,0,0,0.735,"AT5G09970.1","CYP78A7","Cytochrome P450 78A7 ","regulation of growth"]
["isotig78352",{"v":99,"d":"99.00"},53.648,1.131,2.395,0,0,0,0,0,0,"AT1G71050.1","HIPP20","Heavy metal transport/detoxification superfamily protein ","metal ion transport"]

{"sheet":"Up in M1 (E1xM1)","index":1,"n_rows":69,"n_cols":15,"rows_kept":69,"merged":[[3,2,3,6],[3,7,3,10],[37,2,37,6],[37,7,37,10]]}
["Additional file 2: Differentially expressed transcripts (DETs) in embryos and megagametophytes at different stages of seed development. "]
["The Arabidopsis genes showing the highest sequence similarity to the Scots pine transcript are presented (#N/A = no alignment to genes in the TAIR database. Cut off value 1e-5)"]
["The highest up-regulated transcripts in M1/E1. Samples subjected to pairwise comparison are highlighted in bold"]
[null,null,"RPKM Embryos ",{"$nulls":4},"RPKM Megagametophytes ",{"$nulls":5},"Arabidopsis homologous gene names and annotation"]
["Transcript ID","Fold change","E1","E2","E3DO","E3SU","E4","M1","M2","M3","M4","At locus ID","At name","At annotation","Involved in"]
["isotig89204",-6.81314916191854,1.309,21.185,17.765,14.78,26.451,147.198,115.813,149.456,194.321,"AT4G28520.2","CRC","12S seed storage protein CRC","seed maturation; nutrient reservoir activity"]
["isotig96814",-6.65404993703343,1.509,10.682,9.698,7.949,57.309,151.97,104.791,158.734,242.927,"AT1G03880.1","CRB","12S seed storage protein CRB","nutrient reservoir activity; response to ABA"]
["isotig75095",-6.57884263446913,18.252,436.58,296.794,94.556,462.539,1744.775,3192.018,3679.977,4834.673,{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig104606",-6.55624260243997,3.942,25.92,142.208,86.058,269.256,370.973,609.672,716.367,699.314,{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig17379",-6.39979431523284,110.455,1296.884,1045.763,392.882,537.405,9326.43,13142.126,16174.761,14693.908,{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig98072",-6.39807766306689,4.651,65.862,71.979,36.175,244.344,392.247,471.561,542.586,915.363,{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig21345",-6.31900000822589,2.651,40.218,71.001,152.635,346.54,211.65,441.897,424.291,394.603,{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig102265",-6.31549252429835,3.592,29.064,35.917,16.221,8.709,286.081,345.339,438.216,465.397,{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig97641",-6.28417677604137,23.148,99.9,192.9,124.29,598.704,1804.011,1668.846,1608.774,2165.308,{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig87380",-6.2675537770284,3.833,18.091,40.151,20.194,48.531,295.298,333.478,355.597,657.874,{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig90298",-6.25779470793655,1.344,4.078,16.319,5.058,33.672,102.845,58.957,74.211,118.345,{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig91944",-6.24303754808853,1.396,16.944,1.994,1.051,14.667,105.737,181.68,192.713,270.443,"AT1G03890.1","CRD","12S seed storage protein CRD","seed maturation; nutrient reservoir activity"]
["isotig103667",-6.22322610025972,5.638,24.714,56.383,16.976,51.648,421.214,346.3,403.919,466.572,{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig99981",-6.18258032899848,3.271,46.327,23.368,13.544,46.273,237.587,278.674,244.13,485.646,"AT1G03890.1","CRD","12S seed storage protein CRD","seed maturation; nutrient reservoir activity"]
["isotig82381",-6.14275761967682,2.378,31.263,16.133,12.527,37.472,168.022,251.198,238.628,325.021,"AT4G28520.2","CRC","12S seed storage protein CRC","seed maturation; nutrient reservoir activity"]
["isotig110158",-6.06948912325937,23.608,83.579,217.112,108.843,293.378,1585.468,1346.431,1477.655,1786.951,{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig98287",-5.965044251283,1.56,12.623,8.914,2.348,17.651,97.45,151.696,124.554,136.06,{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig87880",-5.93802295015665,2.571,28.61,18.367,6.774,74.819,157.625,162.631,175.573,331.032,"AT1G03880.1","CRB","12S seed storage protein CRB","nutrient reservoir activity; response to ABA"]
["isotig84018",-5.92912344317736,1.217,12.314,26.958,8.247,25.584,74.154,147.768,148.993,154.179,"AT4G28520.1","CRC","12S seed storage protein CRC","seed maturation; nutrient reservoir activity"]
["isotig96258",-5.92880765182252,1.484,31.527,5.301,1.117,13.196,90.403,219.214,200.469,251.446,{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig116865",-5.90990681287464,6.554,86.176,51.493,19.732,90.049,394.063,383.35,440.148,538.65,{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig98597",-5.8531212728768,1.574,33.445,8.997,3.555,22.907,90.985,75.982,65.797,105.641,{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig100751",-5.84605825652489,5.055,35.79,24.07,13.951,73.539,290.777,242.697,204.945,398.496,{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig102309",-5.79264609813484,1.771,26.865,3.794,1.333,32.916,98.17,106.161,84.563,129.195,"AT1G03890.1","CRD","12S seed storage protein CRD","seed maturation; nutrient reservoir activity"]
["isotig105584",-5.77227773466305,2.06,14.584,5.885,9.302,21.642,112.589,67.771,50.722,46.641,{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig93604",-5.73036029940324,1.438,8.725,3.081,0,12.782,76.343,83.045,92.265,155.544,{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig83084",-5.68751312857254,1.203,4.867,12.029,6.338,13.612,61.998,119.62,118.492,149.314,"AT4G28520.1","CRC","12S seed storage protein CRC","seed maturation; nutrient reservoir activity"]
["isotig84240",-5.66068953145528,10.983,45.673,14.819,11.942,51.292,555.595,155.264,96.533,188.328,"AT2G21660.1","RBG7","Glycine-rich RNA-binding protein 7 ","response to external stimulus"]
["isotig93754",-5.62054953849912,2.863,2.896,25.564,14.008,69.424,140.856,84.786,120.716,171.691,{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig84011",-5.62040576421485,2.435,27.092,26.958,15.579,45.264,119.787,178.033,153.535,174.6,"AT4G28520.1","CRC","12S seed storage protein CRC","seed maturation; nutrient reservoir activity"]
[]
["The highest up-regulated transcripts in M1 when E1 RPKM value was equal to 0"]
[null,null,"RPKM Embryos ",{"$nulls":4},"RPKM Megagametophytes ",{"$nulls":5},"Arabidopsis homologous gene names and annotation"]
["ID","Fold change","E1","E2","E3DO","E3SU","E4","M1","M2","M3","M4","At homologous","At Name","At Description","Involved in"]
["isotig109964",-99,0,103.816,103.858,25.752,377.911,476.437,596.195,855.262,1128.601,{"$error":"#N/A"}]
["isotig110695",-99,0,15.101,83.18,58.437,231.688,366.082,342.775,398.853,636.09,{"$error":"#N/A"}]
["isotig105498",-99,0,6.225,24.909,10.808,31.502,179.411,220.484,214.309,378.494,{"$error":"#N/A"}]
["isotig79963",-99,0,16.352,9.898,8.692,25.2,160.511,286.229,248.175,291.512,"AT1G03890.1","CRD","12S seed storage protein CRD","seed maturation; nutrient reservoir activity"]
["isotig108977",-99,0,15.625,22.068,13.566,45.781,150.789,235.315,199.813,222.409,{"$error":"#N/A"}]
["isotig106501",-99,0,8.801,10.876,9.823,58.016,125.692,95.424,76.288,164.182,{"$error":"#N/A"}]
["isotig116039",-99,0,5.735,28.35,17.071,45.828,119.547,157.539,126.934,247.278,{"$error":"#N/A"}]
["isotig97221",-99,0,12.281,30.354,35.414,12.267,118.515,163.125,216.316,266.027,"AT4G28520.2","CRC","12S seed storage protein CRC","seed maturation; nutrient reservoir activity"]
["isotig110991",-99,0,3.112,0,0,17.409,117.738,119.242,121.697,121.29,{"$error":"#N/A"}]
["isotig96023",-99,0,6.014,11.679,8.951,10.812,117.232,176.064,266.206,184.499,{"$error":"#N/A"}]
["isotig89628",-99,0,6.743,8.571,2.007,40.948,105.153,50.691,49.745,107.344,{"$error":"#N/A"}]
["isotig87974",-99,0,7.965,20.624,12.842,40.309,94.288,104.599,94.02,154.1,"AT4G28520.2","CRC","12S seed storage protein CRC","seed maturation; nutrient reservoir activity"]
["isotig111592",-99,0,3.484,14.762,2.593,19.489,94.145,93.188,61.691,132.89,{"$error":"#N/A"}]
["isotig111141",-99,0,9.541,6.737,2.367,12.706,88.388,126.44,110.273,139.757,{"$error":"#N/A"}]
["isotig88478",-99,0,7.863,5.552,3.901,9.424,80.937,191.355,186.593,241.222,"AT1G03890.1","CRD","12S seed storage protein CRD","seed maturation; nutrient reservoir activity"]
["isotig89979",-99,0,9.39,4.737,4.991,15.007,80.78,98.91,99.957,134.587,"AT4G28520.1","CRC","12S seed storage protein CRC","seed maturation; nutrient reservoir activity"]
["isotig02803",-99,0,12.701,17.938,7.089,36.791,79.058,178.462,107.173,182.981,{"$error":"#N/A"}]
["isotig105217",-99,0,16.909,4.478,4.719,6.756,76.691,96.254,96.677,133.189,{"$error":"#N/A"}]
["isotig111359",-99,0,64.816,22.886,33.764,2.59,72.558,203.814,172.147,268.714,{"$error":"#N/A"}]
["isotig103645",-99,0,17.078,8.04,7.06,9.097,71.781,104.245,109.191,121.146,"AT4G28520.1","CRC","12S seed storage protein CRC","seed maturation; nutrient reservoir activity"]
["isotig86638",-99,0,5.136,11.788,4.778,4.104,70.386,43.627,81.472,28.747,{"$error":"#N/A"}]
["isotig55861",-99,0,26.865,10.215,6.151,19.815,70.197,97.098,76.229,126.796,{"$error":"#N/A"}]
["isotig100342",-99,0,20.52,6.038,1.272,8.198,69.968,142.151,126.154,147.455,"AT1G03890.1","CRD","12S seed storage protein CRD","seed maturation; nutrient reservoir activity"]
["isotig116458",-99,0,6.077,17.164,0,9.711,65.677,70.281,94.143,80.614,{"$error":"#N/A"}]
["isotig82658",-99,0,31.94,6.073,1.828,13.743,64.492,103.899,107.851,158.9,"AT1G03890.1","CRD","12S seed storage protein CRD","seed maturation; nutrient reservoir activity"]
["isotig90369",-99,0,9.709,10.774,19.611,35.467,63.179,96.254,93.119,141.458,"AT1G03880.1","CRB","12S seed storage protein CRB","nutrient reservoir activity; response to ABA"]
["isotig116546",-99,0,43.309,39.322,4.604,9.888,62.095,290.707,196.273,328.32,{"$error":"#N/A"}]
["isotig101188",-99,0,8.681,3.678,6.46,81.851,61.656,48.946,49.953,67.658,{"$error":"#N/A"}]
["isotig96781",-99,0,9.115,1.073,4.522,4.856,58.64,175.702,154.663,211.613,{"$error":"#N/A"}]
["isotig109194",-99,0,10.606,16.852,1.973,23.307,57.318,53.669,80.205,70.354,{"$error":"#N/A"}]

{"sheet":"Up in E2 (E2xM2)","index":2,"n_rows":69,"n_cols":15,"rows_kept":69,"merged":[[3,2,3,6],[3,7,3,10],[37,2,37,6],[37,7,37,10]]}
["Additional file 2: Differentially expressed transcripts (DETs) in embryos and megagametophytes at different stages of seed development. "]
["The Arabidopsis genes showing the highest sequence similarity to the Scots pine transcript are presented (#N/A = no alignment to genes in the TAIR database. Cut off value 1e-5)"]
["The highest up-regulated transcripts in E2/M2. Samples subjected to pairwise comparison are highlighted in bold"]
[null,null,"RPKM Embryos ",{"$nulls":4},"RPKM Megagametophytes ",{"$nulls":5},"Arabidopsis homologous gene names and annotation"]
["Transcript ID","Fold change","E1","E2","E3DO","E3SU","E4","M1","M2","M3","M4","At locus ID","At name","At annotation","Involved in"]
["isotig56640",8.36366239332128,366.459,151.191,102.056,132.601,21.066,0.736,0.459,0.469,0.527,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig38581",8.32589615737652,53.73,113.592,69.151,214.241,43.036,0.378,0.354,0.722,2.03,"AT5G09970.1","CYP78A7","Cytochrome P450 78A7 ","regulation of growth"]
["isotig07360",7.71535476063261,71.552,115.799,115.128,326.549,273.941,7.646,0.551,0,3.158,"AT2G18050.1","HIS1-3","histone H1-3 ","nucleosome assembly"]
["isotig60244",7.32670733851707,175.589,119.435,89.067,0.766,9.461,3.577,0.744,0.38,0,"AT4G23560.1","AtGH9B15","Endoglucanase 20 ","cell wall organization"]
["isotig42131",7.32439488253369,24.325,53.852,47.863,51.129,33.015,0,0.336,0,0,"AT3G07010.1",null,"Probable pectate lyase 8 ","pectin catabolic process"]
["isotig75051",7.27568281812542,69.346,120.863,172.985,556.51,468.228,5.832,0.78,0,3.579,"AT2G18050.1","HIS1-3","histone H1-3 ","nucleosome assembly"]
["isotig55225",7.26280071129196,30.481,190.126,68.945,63.732,145.08,6.612,1.238,1.264,1.42,"ATMG00580.1","NAD4","NADH dehydrogenase subunit 4 ","oxidation-reduction process"]
["isotig56593",7.24558153109582,187.22,137.64,88.341,130.891,36.077,0.968,0.907,1.388,1.56,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig40165",7.18342762821095,768.679,486.064,306.871,402.103,158.957,6.667,3.344,5.916,7.416,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig06047",7.16900632674921,13.133,69.076,67.071,86.496,33.436,0,0.48,0,0,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig24350",7.09699644293381,192.239,89.123,132.228,0,0.719,9.73,0.651,1.992,3.732,"AT4G26880.1",null,"Stigma-specific STIG1-like protein 1 ","unknown"]
["isotig92432",7.03756590613688,11.091,133.216,54.463,66.785,110.931,6.496,1.014,2.069,4.651,"ATMG00580.1","NAD4","NADH dehydrogenase subunit 4 ","oxidation-reduction process"]
["isotig66863",7.02295377115362,35.328,76.341,94.628,90.654,41.533,3.135,0.587,0.599,0.673,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig63611",6.9278087560657,28.291,58.563,48.874,87.16,51.05,3.083,0.481,1.964,2.759,"AT2G18050.1","HIS1-3","histone H1-3 ","nucleosome assembly"]
["isotig11848",6.88128467249128,1043.502,656.052,442.745,666.113,166.769,7.264,5.565,4.417,5.319,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig26983",6.82679711550446,64.718,72.539,40.917,33.573,32.163,1.024,0.639,0,1.1,"AT1G76160.1","sks5","SKU5 similar 5 ","plant-type cell wall cellulose metabolic process"]
["isotig51059",6.76293584340583,23.714,150.634,119.246,565.477,340.401,12.592,1.387,2.831,4.773,"AT5G59320.1","LTP3","Non-specific lipid-transfer protein 3 ","response to ABA and abiotic stress"]
["isotig04667",6.67689385135383,32.512,34.276,20.606,17.579,9.993,1.43,0.335,1.709,1.92,"AT1G76160.1","sks5","SKU5 similar 5 ","plant-type cell wall cellulose metabolic process"]
["isotig71086",6.65724818756295,30.171,71.864,75.079,73.99,44.838,1.52,0.712,1.453,1.632,"AT3G46030.1","HTB11","Histone H2B.7 ","nucleosome assembly"]
["isotig80888",6.60963063799972,269.835,417.087,373.798,547.779,787.41,21.892,4.271,2.615,10.777,"ATMG00580.1","NAD4","NADH dehydrogenase subunit 4 ","oxidation-reduction process"]
["isotig43079",6.59658585400499,12.039,35.517,33.322,4.908,15.001,1.959,0.367,1.872,2.104,"AT1G11260.1","STP1","Sugar transport protein 1 ","transmembrane transport"]
["isotig44479",6.5755168965528,1.734,40.343,44.591,9.572,22.893,0.451,0.423,0.431,0,"AT5G48540.1","CRRSP55","Cysteine-rich repeat secretory protein 55 ","response to karrikin"]
["isotig32048",6.49114831124439,5.229,49.116,71.503,34.863,45.889,0.583,0.546,1.115,2.506,"AT4G27250.1",null,"NAD(P)-binding Rossmann-fold superfamily protein ","gibberellin biosynthetic process"]
["isotig03831",6.45314614311823,16.25,111.537,99.077,108.775,83.966,4.985,1.273,3.898,0.487,"AT5G67070.1","RALFL34","Protein RALF-like 34 ","cell-cell signaling; hormone activity"]
["isotig58592",6.33892116580067,22.081,51.24,46.39,69.092,86.788,1.691,0.633,1.292,1.089,"AT1G72830.1","NFYA3","Nuclear transcription factor Y subunit A-3 ","DNA binding"]
["isotig14492",6.31262368759727,56.347,52.858,44.792,17.786,37.83,1.419,0.665,2.374,3.43,"AT1G07290.1","GONST2","GDP-mannose transporter GONST2 ","protein glycosylation"]
["isotig13900",6.30938371656498,21.662,85.652,37.627,70.039,27.854,3.076,1.08,1.47,0.413,"AT1G08880.1","HTA5","Probable histone H2AXa ","nucleosome assembly"]
["isotig57374",6.24993185340798,2.9,20.168,10.099,12.006,13.771,2.831,0.265,0.812,0,"AT3G19240.1",null,"Vacuolar import/degradation, Vid27-related protein ","protein binding"]
["isotig59043",6.19420965356574,12.28,24.383,20.467,10.613,23.16,2.841,0.333,1.018,1.907,"AT3G61490.1",null,"Pectin lyase-like superfamily protein ","cell wall organization"]
["isotig26898",6.18283824685815,14.423,117.834,130.76,40.643,51.114,3.177,1.622,2.484,3.102,"AT5G26340.1","STP13","Sugar transport protein 13 ","response to abiotic stress"]
[]
["The highest up-regulated transcripts in E2 when M2 RPKM value was equal to 0"]
[null,null,"RPKM Embryos ",{"$nulls":4},"RPKM Megagametophytes ",{"$nulls":5},"Arabidopsis homologous gene names and annotation"]
["Transcript ID","Fold change","E1","E2","E3DO","E3SU","E4","M1","M2","M3","M4","At homologous","At Name","At Description","Involved in"]
["isotig101972",99,2337.312,1557.12,774.994,1080.524,331.704,2.751,0,0,1.477,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig87650",99,7.694,585.015,423.194,1747.17,412.532,7.01,0,0,6.453,"AT5G59320.1","LTP3","Non-specific lipid-transfer protein 3 ","response to ABA and abiotic stress"]
["isotig98833",99,980.78,494.428,351.408,472.717,153.43,0,0,1.18,0,"AT5G23870.2","PAE9","Pectin acetylesterase 9 ","cell wall loosening"]
["isotig18163",99,297.588,287.147,411.141,150.315,30.857,0,0,0,0,"AT5G62360.1",0,"Plant invertase/pectin methylesterase inhibitor superfamily protein ","negative regulation of catalytic activity"]
["isotig41809",99,55.68,208.872,124.012,233.316,19.844,0,0,0,0.735,"AT5G09970.1","CYP78A7","Cytochrome P450 78A7 ","regulation of growth"]
["isotig04236",99,32.099,162.718,322.59,587.741,978.037,0.874,0,0,0.939,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig14330",99,234.826,92.652,80.893,23.818,2.019,0,0,0,0,"AT4G38400.1","EXLA2","Expansin-like A2 ","sexual reproduction"]
["isotig113839",99,90.258,91.296,46.888,24.705,13.264,0,0,6.123,0,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig42299",99,344.004,82.784,93.16,206.886,7.429,0.342,0,0.653,0.734,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig45249",99,37.635,80.577,56.005,25.968,14.702,0,0,0,1.052,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig13103",99,15.678,78.299,95.186,92.194,19.799,0,0,0,1.644,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig25556",99,170.334,77.394,85.883,112.444,92.764,0,0,0,0,"AT1G10460.1","GLP7","Germin-like protein subfamily 1 member 1 ","metal ion binding"]
["isotig16733",99,40.055,75.718,75.983,95.887,16.983,0,0,0,0,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig93401",99,292.782,72.613,51.277,117.608,7.964,0,0,0,1.181,"AT1G01190.1","CYP78A8","cytochrome P450, family 78, subfamily A, polypeptide 8 ","oxidation-reduction process"]
["PUT-49222",99,29.002,58.67,29.002,39.294,14.064,9.059,0,0,14.594,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig116979",99,19.789,53.378,75.388,74.479,26.658,20.605,0,4.922,27.662,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig66087",99,7.746,53.276,43.707,1.166,14.399,0.605,0,0,0,"AT3G19430.1",null,"late embryogenesis abundant protein-related / LEA protein-related ","unknown"]
["isotig04574",99,203.454,50.966,34.9,56.315,3.394,0,0,0,0,"AT5G09970.1","CYP78A7","Cytochrome P450 78A7 ","regulation of growth"]
["isotig58929",99,22.488,48.677,26.343,19.297,10.542,0,0,0,0,"AT1G76160.1","sks5","SKU5 similar 5 ","plant-type cell wall cellulose metabolic process"]
["isotig89904",99,12.015,45.912,17.164,46.224,20.501,1.042,0,0,1.12,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig19551",99,84.732,45.71,52.453,39.685,3.044,0,0,0,0,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig73704",99,7.382,44.803,21.845,33.34,17.048,0,0,0,0,"AT5G62040.1","BFT","Protein BROTHER of FT and TFL 1 ","vegetative to reproductive phase transition of meristem"]
["isotig12568",99,0.969,43.128,57.104,27.718,110.827,0,0,0,0,"AT1G77380.1","AAP3","Amino acid permease 3 ","amino acid transmembrane transport"]
["isotig48879",99,25.322,42.993,32.944,34.036,11.695,0,0,0,0,"AT3G54560.1","H2AV","Histone H2A variant 1 ","nucleosome assembly"]
["isotig25890",99,8.571,41.181,24.489,30.645,18.185,0,0,0,0,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig103195",99,0,40.909,64.342,44.28,57.948,0,0,0,0,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig105977",99,4.214,40.493,10.535,7.93,13.624,6.581,0,6.289,12.37,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig66830",99,44.749,40.414,23.402,30.074,13.563,0,0,0,1.34,"AT2G04780.1","FLA7","Fasciclin-like arabinogalactan protein 7 "]
["isotig105225",99,141.863,38.948,21.714,45.764,1.638,0,0,0,0,"AT5G09970.1","CYP78A7","Cytochrome P450 78A7 ","regulation of growth"]
["isotig115879",99,0,38.837,0,0,0,0,0,0,0,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]

{"sheet":"Up in M2 (E2xM2)","index":3,"n_rows":69,"n_cols":15,"rows_kept":69,"merged":[[3,2,3,6],[3,7,3,10],[37,2,37,6],[37,7,37,10]]}
["Additional file 2: Differentially expressed transcripts (DETs) in embryos and megagametophytes at different stages of seed development. "]
["The Arabidopsis genes showing the highest sequence similarity to the Scots pine transcript are presented (#N/A = no alignment to genes in the TAIR database. Cut off value 1e-5)"]
["The highest up-regulated transcripts in M2/E2. Samples subjected to pairwise comparison are highlighted in bold"]
[null,null,"RPKM Embryos ",{"$nulls":4},"RPKM Megagametophytes ",{"$nulls":5},"Arabidopsis homologous gene names and annotation"]
["Transcript ID","Fold change","E1","E2","E3DO","E3SU","E4","M1","M2","M3","M4","At locus ID","At name","At annotation","Involved in"]
["isotig111460",-5.95813475324912,6.428,3.251,41.325,14.516,38.968,102.908,202.113,155.905,272.266,{"$error":"#N/A"}]
["isotig15249",-5.83475337245073,2.522,0.638,0.45,1.424,3.567,16.737,36.413,26.343,54.456,{"$error":"#N/A"}]
["isotig91286",-5.59836816572811,4.059,1.368,3.865,1.018,6.561,54.936,66.277,57.546,118.004,"AT4G28520.1","CRC","12S seed storage protein CRC","seed maturation; nutrient reservoir activity"]
["isotig11912",-5.46149984291552,2.379,0.602,3.398,4.029,4.807,20.435,26.526,23.966,22.944,{"$error":"#N/A"}]
["isotig94827",-5.36455336239723,8.713,1.469,9.335,7.651,14.085,68.04,60.522,58.517,64.549,{"$error":"#N/A"}]
["isotig110991",-5.25990660786185,0,3.112,0,0,17.409,117.738,119.242,121.697,121.29,{"$error":"#N/A"}]
["isotig08500",-5.204198922638,30.359,2.996,6.347,12.262,27.53,221.461,110.449,88.962,95.637,{"$error":"#N/A"}]
["isotig86626",-5.20385920691804,3.789,1.278,2.707,0.951,2.042,18.741,47.103,47.13,43.435,{"$error":"#N/A"}]
["isotig65828",-5.17479499531563,1.51,0.764,1.618,3.409,1.83,20.632,27.597,15.773,19.626,{"$error":"#N/A"}]
["isotig105498",-5.14645631922407,0,6.225,24.909,10.808,31.502,179.411,220.484,214.309,378.494,{"$error":"#N/A"}]
["isotig100247",-5.08644492330725,0,1.668,1.178,0,1.333,30.907,56.672,50.456,84.368,{"$error":"#N/A"}]
["isotig96528",-5.05531834861244,4.479,7.551,83.18,40.456,102.57,174.88,251.077,320.865,313.036,{"$error":"#N/A"}]
["isotig87457",-5.02351657167109,1.279,2.588,5.482,1.926,12.407,38.957,84.177,55.364,92.262,"AT1G03890.1","CRD","12S seed storage protein CRD","seed maturation; nutrient reservoir activity"]
["isotig81937",-5.0231814115453,2.372,1.2,2.541,0.893,0,27.783,39.022,12.39,8.952,{"$error":"#N/A"}]
["isotig40699",-4.97471097981024,3.056,0.687,2.183,1.022,5.215,13.259,21.602,15.205,19.937,"AT2G14740.1","VSR3","Vacuolar-sorting receptor 3","protein targeting to vacuole"]
["isotig108255",-4.96920200118112,4.887,14.831,75.057,75.416,108.633,171.746,464.568,444.955,379.161,{"$error":"#N/A"}]
["isotig13086",-4.9584208962486,11.117,1.606,2.836,4.184,0,34.725,49.932,79.403,73.923,{"$error":"#N/A"}]
["isotig53951",-4.92406493445112,13.979,1.414,17.972,7.365,11.298,26.198,42.928,52.157,113.72,{"$error":"#N/A"}]
["isotig93754",-4.87169255680635,2.863,2.896,25.564,14.008,69.424,140.856,84.786,120.716,171.691,{"$error":"#N/A"}]
["isotig96023",-4.87163127174221,0,6.014,11.679,8.951,10.812,117.232,176.064,266.206,184.499,{"$error":"#N/A"}]
["isotig15915",-4.85408707902308,3.302,1.113,4.324,2.9,1.334,33.949,32.19,21.765,25.384,"AT1G21460.1","SWEET1","Bidirectional sugar transporter SWEET1","carbohydrate transmembrane transport"]
["isotig89551",-4.8539619528628,2.635,2.665,6.588,5.951,14.909,68.935,77.07,74.724,101.662,{"$error":"#N/A"}]
["isotig83926",-4.85367723569414,6.08,4.92,6.08,6.407,3.931,102.551,142.255,137.925,149.914,{"$error":"#N/A"}]
["isotig67718",-4.85323807638002,5.046,0.851,1.201,0,24.472,11.822,24.598,13.808,14.108,{"$error":"#N/A"}]
["isotig101116",-4.83927734972388,8.467,8.564,9.676,2.549,1.369,97.854,245.157,296.96,184.628,{"$error":"#N/A"}]
["isotig70333",-4.81685325546986,1.892,0.957,2.703,0,0,4.432,26.973,12.705,36.492,{"$error":"#N/A"}]
["isotig74245",-4.81651798337245,1.052,1.065,3.007,0,6.805,17.258,30.01,45.55,55.606,"AT1G52240.2","ATROPGEF11","RHO guanyl-nucleotide exchange factor 11 ","microtubule-based process"]
["isotig81044",-4.7984861805758,0,2.366,2.506,5.282,22.686,19.178,65.842,39.272,46.099,"AT2G24762.1","GDU4","Protein GLUTAMINE DUMPER 4 ","regulation of amino acid export"]
["isotig116039",-4.77977172669595,0,5.735,28.35,17.071,45.828,119.547,157.539,126.934,247.278,{"$error":"#N/A"}]
["isotig38068",-4.75673697837031,4.476,5.659,21.579,7.58,17.183,71.648,152.989,137.77,213.959,"AT1G03890.1","CRD","12S seed storage protein CRD ","nutrient reservoir activity"]
[]
["The highest up-regulated transcripts in M2 when E2 RPKM value was equal to 0"]
[null,null,"RPKM Embryos ",{"$nulls":4},"RPKM Megagametophytes ",{"$nulls":5},"Arabidopsis homologous gene names and annotation"]
["ID","Fold change","E1","E2","E3DO","E3SU","E4","M1","M2","M3","M4","At homologous","At Name","At Description","Involved in"]
["isotig111425",-99,9.704,0,11.553,12.174,7.844,169.245,153.739,142.421,143.788,"AT1G76990.1","ACR3","ACT domain-containing protein ACR3","cysteine biosynthetic process"]
["isotig113357",-99,0,0,0,0,3.15,33.472,68.381,43.618,62.095,{"$error":"#N/A"}]
["isotig107041",-99,0,0,0,7.034,16.994,31.014,56.371,31.381,33.309,{"$error":"#N/A"}]
["isotig93861",-99,1.414,0,10.097,4.256,11.425,38.634,54.778,81.221,61.646,{"$error":"#N/A"}]
["isotig115197",-99,0,0,14.066,0,39.792,11.534,50.396,36.739,53.677,{"$error":"#N/A"}]
["isotig103400",-99,0,0,0,0,0,31.169,48.641,56.734,121.149,{"$error":"#N/A"}]
["isotig102633",-99,0,0,0,0,0,25.333,44.804,60.52,71.041,{"$error":"#N/A"}]
["isotig95840",-99,1.471,0,3.153,3.322,4.756,24.126,43.029,19.762,60.461,{"$error":"#N/A"}]
["isotig114762",-99,0,0,0,0,0,54.087,39.791,95.989,70.538,{"$error":"#N/A"}]
["isotig103518",-99,3.724,0,5.32,2.803,9.03,33.444,39.484,33.349,35.919,{"$error":"#N/A"}]
["isotig108157",-99,0,0,0,3.661,3.931,15.193,39.12,19.963,38.753,{"$error":"#N/A"}]
["isotig88459",-99,5.189,0,0.927,3.906,3.146,5.065,37.941,61.955,57.663,{"$error":"#N/A"}]
["isotig111394",-99,0,0,2.281,0,0,27.435,37.364,45.284,42.858,{"$error":"#N/A"}]
["isotig55863",-99,0,0,3.972,0,4.494,32.567,36.592,37.346,25.65,{"$error":"#N/A"}]
["isotig116304",-99,0,0,0,4.495,0,32.644,34.932,31.195,45.077,{"$error":"#N/A"}]
["isotig109530",-99,2.699,0,13.493,6.094,8.724,31.609,33.543,14.096,29.422,"AT3G02470.1","SAMDC1","S-adenosylmethionine decarboxylase proenzyme 1 ","spermidine biosynthetic process"]
["isotig49875",-99,0,0,4.123,1.448,3.888,27.047,33.063,25.129,24.207,"AT2G01300.1","unknown protein"]
["isotig105366",-99,10.194,0,4.369,3.069,6.592,50.95,32.798,38.037,32.49,"AT1G80760.1","NIP6-1","Aquaporin NIP6-1 ","water transport"]
["isotig114480",-99,0,0,3.176,0,3.594,10.416,32.509,69.674,108.137,{"$error":"#N/A"}]
["isotig111247",-99,0,0,2.253,0,2.549,27.092,32.285,61.193,31.742,{"$error":"#N/A"}]
["isotig108267",-99,4.887,0,5.237,1.839,3.95,34.349,32.162,58.355,34.842,{"$error":"#N/A"}]
["isotig96314",-99,0,0,2.198,2.316,4.974,33.639,31.498,25.258,15.484,{"$error":"#N/A"}]
["isotig96969",-99,3.026,0,0,0,0,11.816,30.978,21.454,12.69,{"$error":"#N/A"}]
["isotig114674",-99,5.229,0,3.735,7.872,0,16.334,30.589,31.218,39.472,{"$error":"#N/A"}]
["isotig36963",-99,0,0,5.923,2.675,2.872,12.025,28.582,25.635,22.85,{"$error":"#N/A"}]
["isotig115110",-99,0,0,0,0,3.922,22.734,28.383,36.209,32.556,{"$error":"#N/A"}]
["isotig83588",-99,1.226,0,1.752,0,0,16.28,26.003,10.981,16.456,{"$error":"#N/A"}]
["isotig112494",-99,0,0,5.041,7.969,0,16.534,25.802,28.967,35.515,{"$error":"#N/A"}]
["isotig80019",-99,1.157,0,0,0,2.806,3.615,25.388,33.684,27.18,{"$error":"#N/A"}]
["isotig14517",-99,0.526,0,1.878,0.792,4.251,22.588,24.996,33.752,21.613,{"$error":"#N/A"}]

{"sheet":"Up in E3DO (E3DOxM3)","index":4,"n_rows":69,"n_cols":15,"rows_kept":69,"merged":[[3,2,3,6],[3,7,3,10],[37,2,37,6],[37,7,37,10]]}
["Additional file 2: Differentially expressed transcripts (DETs) in embryos and megagametophytes at different stages of seed development. "]
["The Arabidopsis genes showing the highest sequence similarity to the Scots pine transcript are presented (#N/A = no alignment to genes in the TAIR database. Cut off value 1e-5)"]
["The highest up-regulated transcripts in E3DO/M3. Samples subjected to pairwise comparison are highlighted in bold"]
[null,null,"RPKM Embryos ",{"$nulls":4},"RPKM Megagametophytes ",{"$nulls":5},"Arabidopsis homologous gene names and annotation"]
["Transcript ID","Fold change","E1","E2","E3DO","E3SU","E4","M1","M2","M3","M4","At locus ID","At name","At annotation","Involved in"]
["isotig98833",8.21821636566865,980.78,494.428,351.408,472.717,153.43,0,0,1.18,0,"AT5G23870.2","PAE9","Pectin acetylesterase 9 ","cell wall loosening"]
["isotig60244",7.87274777249436,175.589,119.435,89.067,0.766,9.461,3.577,0.744,0.38,0,"AT4G23560.1","AtGH9B15","Endoglucanase 20 ","cell wall organization"]
["isotig56640",7.76555736463295,366.459,151.191,102.056,132.601,21.066,0.736,0.459,0.469,0.527,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig66863",7.30356732047478,35.328,76.341,94.628,90.654,41.533,3.135,0.587,0.599,0.673,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig80888",7.15930409329034,269.835,417.087,373.798,547.779,787.41,21.892,4.271,2.615,10.777,"ATMG00580.1","NAD4","NADH dehydrogenase subunit 4 ","oxidation-reduction process"]
["isotig42299",7.1564838375518,344.004,82.784,93.16,206.886,7.429,0.342,0,0.653,0.734,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig60442",7.02589066976695,30.111,57.239,50.433,34.389,25.597,1.622,1.898,0.387,1.306,"AT3G45310.1",0,"Thiol protease aleurain-like ","proteolysis involved in cellular protein catabolic process"]
["isotig63780",6.9807154348459,95.012,57.797,62.645,5.001,5.37,1.557,3.886,0.496,1.114,"AT5G60530.1",0,"late embryogenesis abundant protein-related / LEA protein-related ","transition metal ion transport"]
["isotig83308",6.8244237478032,822.445,673.619,1025.89,1868.158,1106.928,57.783,18.626,9.052,15.261,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig44479",6.69292087442623,1.734,40.343,44.591,9.572,22.893,0.451,0.423,0.431,0,"AT5G48540.1","CRRSP55","Cysteine-rich repeat secretory protein 55 ","esponse to karrikin"]
["isotig11848",6.64726537184774,1043.502,656.052,442.745,666.113,166.769,7.264,5.565,4.417,5.319,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig38581",6.58160746715604,53.73,113.592,69.151,214.241,43.036,0.378,0.354,0.722,2.03,"AT5G09970.1","CYP78A7","Cytochrome P450 78A7 ","regulation of growth"]
["isotig28506",6.37984763597639,2.573,34.484,39.973,58.586,48.351,0.502,0,0.48,0,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig34646",6.3759343199446,426.889,167.432,166.103,35.311,93.707,16.746,4.41,2,4.496,"AT4G01610.1",0,"Cysteine proteinases superfamily protein ","cell morphogenesis; cell growth"]
["isotig55937",6.3123101769167,14.336,22.235,56.661,12.949,26.264,2.985,0.699,0.713,0.802,"AT1G28330.1","DYL1","dormancy-associated protein-like 1 ","unknown"]
["isotig70648",6.27586797174337,31.114,35.405,56.255,50.499,24.362,1.519,1.422,0.726,0,"AT3G57440.1",0,"unknown","unknown"]
["isotig55932",6.27519333390221,8.621,20.554,35.627,37.08,18.913,5.77,2.251,0.46,1.549,"AT2G39795.1",0,"Uncharacterized protein At2g39795, mitochondrial ","unknown"]
["isotig62762",6.2577697925709,373.053,22.234,35.888,1.418,5.076,3.433,1.378,0.469,3.16,"AT1G69830.1","AMY3","Alpha-amylase 3, chloroplastic ","carbohydrate metabolic process"]
["isotig78926",6.25005506882236,88.551,87.272,128.934,17.945,13.764,0,1.66,1.694,0.952,"AT5G62360.1",0,"Plant invertase/pectin methylesterase inhibitor superfamily protein ","negative regulation of catalytic activity"]
["isotig113860",6.14611261456988,53.335,336.136,216.855,200.729,437.711,32.038,11.999,3.062,6.882,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig39079",6.06524530937418,15.074,25.413,35.891,15.669,19.146,0,0,0.536,0,"AT1G20190.1","EXPA11","Expansin-A11 ","plant-type cell wall organization"]
["isotig24350",6.05266625010589,192.239,89.123,132.228,0,0.719,9.73,0.651,1.992,3.732,"AT4G26880.1",0,"Stigma-specific STIG1-like protein 1 ","unknown"]
["isotig78934",6.02448383405608,51.202,82.866,55.266,75.369,123.234,3.554,1.664,0.849,3.817,"ATMG00580.1","NAD4","NADH dehydrogenase subunit 4 ","oxidation-reduction process"]
["isotig32048",6.00288815802199,5.229,49.116,71.503,34.863,45.889,0.583,0.546,1.115,2.506,"AT4G27250.1",0,"NAD(P)-binding Rossmann-fold superfamily protein ","gibberellin biosynthetic process"]
["isotig114214",5.99868128589265,650.028,333.077,1020.251,2343.423,1023.125,33.395,18.761,15.956,14.347,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig39384",5.99620214397771,34.002,128.715,73.598,140.768,84.114,8.046,4.52,1.153,7.345,"AT4G32460.1",0,"Protein of unknown function, DUF642 ","unknown"]
["isotig56593",5.99200369042097,187.22,137.64,88.341,130.891,36.077,0.968,0.907,1.388,1.56,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig64994",5.96057154069578,10.844,9.507,33.566,0.544,7.012,0,0.529,0.539,0.606,"AT1G14520.1","MIOX1","Inositol oxygenase 1 ","oxidation-reduction process"]
["isotig23092",5.95853789840112,36.7,37.122,42.598,89.78,22.989,9.314,0,0.685,3.078,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig21539",5.93624963062748,28.766,20.22,22.289,1.468,4.729,0.381,0,0.364,1.227,"AT3G26200.1","CYP71B22","Cytochrome P450 71B22 ","oxidation-reduction process"]
[]
["The highest up-regulated transcripts in E3DO when M3 RPKM value was equal to 0"]
[null,null,"RPKM Embryos ",{"$nulls":4},"RPKM Megagametophytes ",{"$nulls":5},"Arabidopsis homologous gene names and annotation"]
["Transcript ID","Fold change","E1","E2","E3DO","E3SU","E4","M1","M2","M3","M4","At Transcript ID","At Name","At Description","Involved in"]
["isotig101972",99,2337.312,1557.12,774.994,1080.524,331.704,2.751,0,0,1.477,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig87650",99,7.694,585.015,423.194,1747.17,412.532,7.01,0,0,6.453,"AT5G59320.1","LTP3","Non-specific lipid-transfer protein 3 ","response to abscisic acid; response to water deprivation"]
["isotig18163",99,297.588,287.147,411.141,150.315,30.857,0,0,0,0,"AT5G62360.1",0,"Plant invertase/pectin methylesterase inhibitor superfamily protein ","negative regulation of catalytic activity"]
["isotig04236",99,32.099,162.718,322.59,587.741,978.037,0.874,0,0,0.939,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig75051",99,69.346,120.863,172.985,556.51,468.228,5.832,0.78,0,3.579,"AT2G18050.1","HIS1-3","histone H1-3 ","nucleosome assembly"]
["isotig41809",99,55.68,208.872,124.012,233.316,19.844,0,0,0,0.735,"AT5G09970.1","CYP78A7","Cytochrome P450 78A7 ","regulation of growth"]
["isotig07360",99,71.552,115.799,115.128,326.549,273.941,7.646,0.551,0,3.158,"AT2G18050.1","HIS1-3","histone H1-3 ","nucleosome assembly"]
["PUT-58056",99,58.629,122.842,101.703,138.697,16.924,16.351,6.124,0,7.024,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig13103",99,15.678,78.299,95.186,92.194,19.799,0,0,0,1.644,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig73073",99,28.689,84.985,87.093,125.714,53.002,1.6,1.498,0,0.859,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig25556",99,170.334,77.394,85.883,112.444,92.764,0,0,0,0,"AT1G10460.1","GLP7","Germin-like protein subfamily 1 member 1 ","nutrient reservoir activity"]
["isotig14330",99,234.826,92.652,80.893,23.818,2.019,0,0,0,0,"AT4G38400.1","EXLA2","Expansin-like A2 ","sexual reproduction"]
["isotig16733",99,40.055,75.718,75.983,95.887,16.983,0,0,0,0,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["PUT-37504",99,65.643,45.648,73.262,86.468,6.632,19.223,3,0,10.323,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig44201",99,182.288,35.528,72.725,56.892,11.859,0,0,0,0.746,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig06047",99,13.133,69.076,67.071,86.496,33.436,0,0.48,0,0,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig21693",99,35.633,33.923,65.876,32.344,8.471,2.455,2.299,0,0,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig103195",99,0,40.909,64.342,44.28,57.948,0,0,0,0,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig10842",99,16.356,25.302,62.537,2.173,34.993,0,0,0,0,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig12568",99,0.969,43.128,57.104,27.718,110.827,0,0,0,0,"AT1G77380.1","AAP3","Amino acid permease 3 ","amino acid transmembrane transport"]
["isotig71172",99,208.104,29.647,56.527,19.856,14.214,0,0,0,0,"AT5G67070.1","RALFL34","Protein RALF-like 34 ","cell-cell signaling; hormone activity"]
["isotig45249",99,37.635,80.577,56.005,25.968,14.702,0,0,0,1.052,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["PUT-1873",99,11.69,11.825,55.668,35.198,22.047,0,0,0,0,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["PUT-27362",99,63.078,82.033,54.711,88.177,138.384,3.518,3.294,0,7.558,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig114285",99,12.995,26.288,52.598,45.646,42.012,13.53,12.669,0,25.43,"AT1G09330.1","ECH","Golgi apparatus membrane protein-like protein ECHIDNA ","unidimensional cell growth"]
["isotig19551",99,84.732,45.71,52.453,39.685,3.044,0,0,0,0,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig93401",99,292.782,72.613,51.277,117.608,7.964,0,0,0,1.181,"AT1G01190.1","CYP78A8","cytochrome P450, family 78, subfamily A, polypeptide 8 ","regulation of growth"]
["isotig68357",99,13.017,37.745,48.349,45.071,10.521,0,0,0,0,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig28907",99,7.996,39.54,48.229,96.298,98.376,0,0.65,0,1.49,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig42131",99,24.325,53.852,47.863,51.129,33.015,0,0.336,0,0,"AT3G07010.1",0,"Probable pectate lyase 8 ","pectin catabolic process"]

{"sheet":"Up in M3 (E3DOxM3)","index":5,"n_rows":69,"n_cols":15,"rows_kept":69,"merged":[[3,2,3,6],[3,7,3,10],[37,2,37,6],[37,7,37,10]]}
["Additional file 2: Differentially expressed transcripts (DETs) in embryos and megagametophytes at different stages of seed development. "]
["The Arabidopsis genes showing the highest sequence similarity to the Scots pine transcript are presented (#N/A = no alignment to genes in the TAIR database. Cut off value 1e-5)"]
["The highest up-regulated transcripts in M3/E3DO. Samples subjected to pairwise comparison are highlighted in bold"]
[null,null,"RPKM Embryos ",{"$nulls":4},"RPKM Megagametophytes ",{"$nulls":5},"Arabidopsis homologous gene names and annotation"]
["Transcript ID","Fold change","E1","E2","E3DO","E3SU","E4","M1","M2","M3","M4","At locus ID","At name","At annotation","Involved in"]
["isotig96781",-7.17133421608448,0,9.115,1.073,4.522,4.856,58.64,175.702,154.663,211.613,{"$error":"#N/A"}]
["isotig91944",-6.59464467602581,1.396,16.944,1.994,1.051,14.667,105.737,181.68,192.713,270.443,"AT1G03890.1","CRD","12S seed storage protein CRD ","seed maturation; nutrient reservoir activity"]
["isotig107909",-6.51453073999866,14.282,40.931,3.4,0,0,55.764,127.052,310.848,135.751,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig108390",-6.27262658967036,30.661,23.26,1.825,7.693,14.456,129.691,132.644,141.095,212.148,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig83823",-6.1975608777034,6.073,20.884,3.47,7.313,24.541,131.828,255.751,254.672,408.456,"AT1G03890.1","CRD","12S seed storage protein CRD ","seed maturation; nutrient reservoir activity"]
["isotig98332",-6.15027903925651,0,8.381,1.184,2.495,12.055,53.059,102.998,84.095,136.21,"AT4G28520.2","CRC","12S seed storage protein CRC ","seed maturation; nutrient reservoir activity"]
["isotig101482",-6.10722333382539,8.776,12.428,1.254,3.964,7.093,57.567,111.655,86.448,131.016,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig88459",-6.0625075688688,5.189,0,0.927,3.906,3.146,5.065,37.941,61.955,57.663,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig106733",-5.97000270455035,2.283,32.335,1.631,0,27.683,108.768,71.791,102.236,151.289,"AT4G28520.2","CRC","12S seed storage protein CRC "]
["isotig15249",-5.87135084063403,2.522,0.638,0.45,1.424,3.567,16.737,36.413,26.343,54.456,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig106007",-5.87062635584389,6.334,10.678,1.508,1.589,13.652,49.464,77.191,88.234,72.603,"AT4G28520.1","CRC","12S seed storage protein CRC ","seed maturation; nutrient reservoir activity"]
["isotig80506",-5.84460503850469,4.646,11.748,1.659,6.994,10.326,47.161,105.3,95.334,135.393,"AT1G03890.1","CRD","12S seed storage protein CRD ","seed maturation; nutrient reservoir activity"]
["isotig112834",-5.84446186408835,14.627,22.193,2.612,5.505,38.422,94.232,136.36,150.083,171.744,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig20740",-5.73679092317612,17.94,2.927,0.413,0,0.935,18.528,22.003,22.024,27.665,"AT4G26740.1","PXG1","Peroxygenase 1 ","plant seed peroxidase activity"]
["isotig13456",-5.70667595179455,0.332,2.354,0.475,0,11.016,5.971,17.015,24.807,20.353,"AT4G38620.1","MYB4","Transcription repressor MYB4 ","response to hormones"]
["isotig102531",-5.61768261671557,1.828,11.096,1.306,0,4.433,51.399,56.148,64.126,62.87,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig92841",-5.571072752807,5.553,16.85,1.983,3.135,2.244,22.766,66.994,94.272,59.38,"AT5G01380.1","GT-3A","Trihelix transcription factor GT-3a ","transcription"]
["isotig103533",-5.52256264245829,3.78,9.559,1.35,1.423,4.583,85.602,62.187,62.057,58.649,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig32252",-5.49009708083355,0,3.184,0.749,3.159,4.24,14.747,28.383,33.664,25.517,"AT4G36850.1",0,"PQ-loop repeat family protein / transmembrane family protein ","unknown"]
["isotig99566",-5.45598656208877,3.23,9.8,1.153,0,13.052,26.481,61.397,50.611,44.693,"AT1G03890.1","CRD","12S seed storage protein CRD ","seed maturation; nutrient reservoir activity"]
["isotig68989",-5.45581734942118,0.916,5.558,0.654,2.757,8.883,11.443,31.473,28.704,26.884,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig100247",-5.42061439404068,0,1.668,1.178,0,1.333,30.907,56.672,50.456,84.368,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig107511",-5.38474058729238,0,4.672,1.65,1.738,0,30.659,25.33,68.937,67.794,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig94770",-5.27246738166615,1.438,14.542,2.054,5.411,12.782,49.398,72.533,79.391,91.639,"AT4G28520.1","CRC","12S seed storage protein CRC ","seed maturation; nutrient reservoir activity"]
["isotig08295",-5.27128665648024,2.462,4.27,0.503,0.265,2.559,15.383,19.806,19.426,23.308,"AT1G10520.1",0,"DNA polymerase lambda (POLL) ","DNA repair; regulation of chromosome organization"]
["isotig96258",-5.24097080851728,1.484,31.527,5.301,1.117,13.196,90.403,219.214,200.469,251.446,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig45859",-5.23355021122097,2.706,1.368,0.483,0,2.187,13.734,19.784,18.172,11.914,"AT5G15720.1","GLIP7","GDSL esterase/lipase 7 ","lipid catabolic process"]
["isotig74390",-5.19327111181678,1.059,1.071,0.756,0,0.856,11.578,20.907,27.66,33.751,"AT4G23160.1","CRK8","cysteine-rich RLK (RECEPTOR-like protein kinase) 8 ","protein phosphorylation"]
["isotig108473",-5.1927240489803,2.498,7.581,1.784,7.522,40.383,52.672,65.758,65.247,104.759,"AT5G22470.1","PARP3","Poly ","double-strand break repair"]
["isotig112237",-5.1926496596648,3.445,3.484,2.46,0,19.489,34.968,50.372,89.966,54.889,"AT1G03890.1","CRD","12S seed storage protein CRD ","seed maturation; nutrient reservoir activity"]
[]
["The highest up-regulated transcripts in M3 when E3DO RPKM value was equal to 0"]
[null,null,"RPKM Embryos ",{"$nulls":4},"RPKM Megagametophytes ",{"$nulls":5},"Arabidopsis homologous gene names and annotation"]
["ID","Fold change","E1","E2","E3DO","E3SU","E4","M1","M2","M3","M4","At homologous","At Name","At Description","Involved in"]
["isotig110991",-99,0,3.112,0,0,17.409,117.738,119.242,121.697,121.29,{"$error":"#N/A"}]
["isotig111318",-99,3.342,6.761,0,2.515,2.701,23.487,114.846,114.717,81.282,{"$error":"#N/A"}]
["isotig114762",-99,0,0,0,0,0,54.087,39.791,95.989,70.538,{"$error":"#N/A"}]
["isotig113148",-99,3.809,7.705,0,11.467,3.078,62.455,136.451,85.261,73.466,{"$error":"#N/A"}]
["isotig13374",-99,2.429,2.457,0,0,0,32.246,55.057,62.535,78.432,{"$error":"#N/A"}]
["isotig102633",-99,0,0,0,0,0,25.333,44.804,60.52,71.041,{"$error":"#N/A"}]
["isotig103400",-99,0,0,0,0,0,31.169,48.641,56.734,121.149,{"$error":"#N/A"}]
["isotig101744",-99,0,5.568,0,0,1.483,22.927,38.91,46.558,10.773,{"$error":"#N/A"}]
["isotig102224",-99,17.706,100.295,0,1.333,10.018,80.195,69.911,44.924,50.49,{"$error":"#N/A"}]
["isotig113357",-99,0,0,0,0,3.15,33.472,68.381,43.618,62.095,{"$error":"#N/A"}]
["isotig115996",-99,5.638,28.516,0,0,9.114,26.418,57.717,42.075,37.83,{"$error":"#N/A"}]
["isotig113006",-99,7.476,26.467,0,0,3.021,8.757,40.997,41.841,109.725,{"$error":"#N/A"}]
["isotig110213",-99,0,3.753,0,0,2.999,14.488,37.983,38.765,18.672,{"$error":"#N/A"}]
["isotig108366",-99,0,7.488,0,0,5.983,1.927,23.456,36.828,41.391,{"$error":"#N/A"}]
["isotig116517",-99,12.16,6.15,0,18.306,14.742,23.739,4.445,36.296,30.595,{"$error":"#N/A"}]
["isotig115110",-99,0,0,0,0,3.922,22.734,28.383,36.209,32.556,{"$error":"#N/A"}]
["isotig80019",-99,1.157,0,0,0,2.806,3.615,25.388,33.684,27.18,{"$error":"#N/A"}]
["isotig94816",-99,1.491,7.54,0,0,4.82,15.134,33.791,32.262,53.763,"AT1G03890.1",{"$f":"VLOOKUP(L57,[2]Sheet1!$A$2:$C$13,2,FALSE)","v":"CRD"},{"$f":"VLOOKUP(L57,[2]Sheet1!$A$2:$C$13,3,FALSE)","v":"12S seed storage protein CRD "},"seed maturation; nutrient reservoir activity"]
["isotig104997",-99,2.035,6.175,0,1.532,1.645,12.712,35.707,31.887,78.501,{"$error":"#N/A"}]
["isotig107041",-99,0,0,0,7.034,16.994,31.014,56.371,31.381,33.309,{"$error":"#N/A"}]
["isotig116304",-99,0,0,0,4.495,0,32.644,34.932,31.195,45.077,{"$error":"#N/A"}]
["isotig72585",-99,3.331,4.492,0,3.343,1.795,26.878,55.204,30.656,54.009,{"$error":"#N/A"}]
["isotig115394",-99,5.046,5.104,0,0,8.157,23.644,18.449,30.126,33.858,{"$error":"#N/A"}]
["PUT-62775",-99,13.164,4.439,0,13.212,3.547,17.133,9.625,29.471,25.762,{"$error":"#N/A"}]
["isotig93842",-99,1.416,2.864,0,4.262,4.576,7.738,14.49,28.52,28.492,{"$error":"#N/A"}]
["isotig114894",-99,4.716,0,0,3.55,7.624,29.463,13.793,28.155,11.866,{"$error":"#N/A"}]
["isotig78986",-99,1.14,2.307,0,0.858,3.687,5.343,21.68,28.083,9.564,{"$error":"#N/A"}]
["isotig73153",-99,1.029,2.081,0,0,2.495,7.231,17.302,27.638,32.788,"AT5G25940.1",{"$f":"VLOOKUP(L67,[2]Sheet1!$A$2:$C$13,2,FALSE)","v":0},{"$f":"VLOOKUP(L67,[2]Sheet1!$A$2:$C$13,3,FALSE)","v":"early nodulin-related "},"response to ethylene"]
["isotig97152",-99,1.515,4.598,0,0,1.225,13.017,23.269,27.14,40.67,{"$error":"#N/A"}]
["isotig115519",-99,0,0,0,0,0,4.021,11.295,26.898,8.637,{"$error":"#N/A"}]

{"sheet":"Up in E3SU (E3SUxM3)","index":6,"n_rows":69,"n_cols":15,"rows_kept":69,"merged":[[3,2,3,6],[3,7,3,10],[37,2,37,6],[37,7,37,10]]}
["Additional file 2: Differentially expressed transcripts (DETs) in embryos and megagametophytes at different stages of seed development. "]
["The Arabidopsis genes showing the highest sequence similarity to the Scots pine transcript are presented (#N/A = no alignment to genes in the TAIR database. Cut off value 1e-5)"]
["The highest up-regulated transcripts in E3SU/M3. Samples subjected to pairwise comparison are highlighted in bold"]
[null,null,"RPKM Embryos ",{"$nulls":4},"RPKM Megagametophytes ",{"$nulls":5},"Arabidopsis homologous gene names and annotation"]
["Transcript ID","Fold change","E1","E2","E3DO","E3SU","E4","M1","M2","M3","M4","At locus ID","At name","At annotation","Involved in"]
["isotig98833",8.64604607847776,980.78,494.428,351.408,472.717,153.43,0,0,1.18,0,"AT5G23870.2","PAE9","Pectin acetylesterase 9 ","cell wall loosening"]
["isotig42299",8.30753731404795,344.004,82.784,93.16,206.886,7.429,0.342,0,0.653,0.734,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig38581",8.21302004732223,53.73,113.592,69.151,214.241,43.036,0.378,0.354,0.722,2.03,"AT5G09970.1","CYP78A7","Cytochrome P450 78A7 ","regulation of growth"]
["isotig56640",8.14328801738401,366.459,151.191,102.056,132.601,21.066,0.736,0.459,0.469,0.527,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig80888",7.71063920234217,269.835,417.087,373.798,547.779,787.41,21.892,4.271,2.615,10.777,"ATMG00580.1","NAD4","NADH dehydrogenase subunit 4 ","oxidation-reduction process"]
["isotig83308",7.68916417661283,822.445,673.619,1025.89,1868.158,1106.928,57.783,18.626,9.052,15.261,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig51059",7.64201278630098,23.714,150.634,119.246,565.477,340.401,12.592,1.387,2.831,4.773,"AT5G59320.1","LTP3","Non-specific lipid-transfer protein 3 ","response to abscisic acid; response to water deprivation"]
["isotig66863",7.24167086533845,35.328,76.341,94.628,90.654,41.533,3.135,0.587,0.599,0.673,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig11848",7.23655629552056,1043.502,656.052,442.745,666.113,166.769,7.264,5.565,4.417,5.319,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig114214",7.19837455287785,650.028,333.077,1020.251,2343.423,1023.125,33.395,18.761,15.956,14.347,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig23092",7.03414629795502,36.7,37.122,42.598,89.78,22.989,9.314,0,0.685,3.078,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig38237",6.98949202979957,29.401,24.878,12.52,26.812,4.341,0.662,0.827,0.211,0.237,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig39384",6.93178308825835,34.002,128.715,73.598,140.768,84.114,8.046,4.52,1.153,7.345,"AT4G32460.1",null,"Protein of unknown function, DUF642 ","unknown"]
["isotig28506",6.93137773623939,2.573,34.484,39.973,58.586,48.351,0.502,0,0.48,0,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig71492",6.78076993561597,25.576,24.875,37.942,80.707,19.877,29.958,3.596,0.734,4.125,"AT3G42725.1",null,"Putative membrane lipoprotein ","unknown"]
["isotig48361",6.68623114149653,2.79,31.042,31.387,53.55,17.476,0,1.53,0.52,1.17,"AT1G59940.1","ARR3","Two-component response regulator ARR3 ","response to cytokinin; circadian rhythm"]
["isotig56593",6.55921452355917,187.22,137.64,88.341,130.891,36.077,0.968,0.907,1.388,1.56,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig27288",6.51903206441907,11.327,23.488,25.486,38.794,38.452,7.519,1.656,0.423,3.325,"AT5G38110.1","ASF1B","Histone chaperone ASF1B ","regulation of cell size; cell division"]
["isotig60442",6.47346978765541,30.111,57.239,50.433,34.389,25.597,1.622,1.898,0.387,1.306,"AT3G45310.1",null,"Thiol protease aleurain-like ","proteolysis"]
["isotig78934",6.4720628870418,51.202,82.866,55.266,75.369,123.234,3.554,1.664,0.849,3.817,"ATMG00580.1","NAD4","NADH dehydrogenase subunit 4 ","oxidation-reduction process"]
["isotig55932",6.33286357256852,8.621,20.554,35.627,37.08,18.913,5.77,2.251,0.46,1.549,"AT2G39795.1",null,"Uncharacterized protein At2g39795, mitochondrial ","unknown"]
["isotig60559",6.31806840778257,37.438,17.601,19.209,31.356,0.852,0,0,0.393,0.442,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig21424",6.26073863146318,4.461,4.512,0.797,63.796,130.698,0.871,0,0.832,0,"AT5G59320.1","LTP3","Non-specific lipid-transfer protein 3 ","response to abscisic acid; response to water deprivation"]
["isotig43821",6.25920522068762,5.249,8.343,16.068,21.447,48.18,1.171,1.371,0.28,0.314,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig34581",6.20359665288201,12.666,13.486,26.665,36.629,32.328,9.891,4.874,0.497,3.354,"AT4G19350.1","EMB3006","embryo defective 3006 ","unknown"]
["isotig70648",6.12014146091664,31.114,35.405,56.255,50.499,24.362,1.519,1.422,0.726,0,"AT3G57440.1",null,"unknown","unknown"]
["isotig52803",6.09988487524365,3.425,8.084,22.018,58.437,22.147,2.675,0,0.852,0,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig40165",6.08679923713923,768.679,486.064,306.871,402.103,158.957,6.667,3.344,5.916,7.416,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig49156",6.05642134579738,0,9.418,9.31,46.254,10.535,0,0,0.695,0,"AT1G73580.1",null,"Calcium-dependent lipid-binding (CaLB domain) family protein ","unknown"]
["isotig113860",6.03463096974513,53.335,336.136,216.855,200.729,437.711,32.038,11.999,3.062,6.882,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
[]
["The highest up-regulated transcripts in E3SU when M3 RPKM value was equal to 0"]
[null,null,"RPKM Embryos ",{"$nulls":4},"RPKM Megagametophytes ",{"$nulls":5},"Arabidopsis homologous gene names and annotation"]
["Transcript ID","Fold change","E1","E2","E3DO","E3SU","E4","M1","M2","M3","M4","At Transcript ID","At Name","At Description","Involved in"]
["isotig87650",99,7.694,585.015,423.194,1747.17,412.532,7.01,0,0,6.453,"AT5G59320.1","LTP3","Non-specific lipid-transfer protein 3 ","response to abscisic acid; response to water deprivation"]
["isotig101972",99,2337.312,1557.12,774.994,1080.524,331.704,2.751,0,0,1.477,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig04236",99,32.099,162.718,322.59,587.741,978.037,0.874,0,0,0.939,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig75051",99,69.346,120.863,172.985,556.51,468.228,5.832,0.78,0,3.579,"AT2G18050.1","HIS1-3","histone H1-3 ","nucleosome assembly"]
["isotig07360",99,71.552,115.799,115.128,326.549,273.941,7.646,0.551,0,3.158,"AT2G18050.1","HIS1-3","histone H1-3 ","nucleosome assembly"]
["isotig41809",99,55.68,208.872,124.012,233.316,19.844,0,0,0,0.735,"AT5G09970.1","CYP78A7","Cytochrome P450 78A7 ","regulation of growth"]
["isotig18163",99,297.588,287.147,411.141,150.315,30.857,0,0,0,0,"AT5G62360.1",null,"Plant invertase/pectin methylesterase inhibitor superfamily protein ","negative regulation of catalytic activity"]
["PUT-58056",99,58.629,122.842,101.703,138.697,16.924,16.351,6.124,0,7.024,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig73073",99,28.689,84.985,87.093,125.714,53.002,1.6,1.498,0,0.859,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig93401",99,292.782,72.613,51.277,117.608,7.964,0,0,0,1.181,"AT1G01190.1","CYP78A8","cytochrome P450, family 78, subfamily A, polypeptide 8 ","regulation of growth"]
["isotig25556",99,170.334,77.394,85.883,112.444,92.764,0,0,0,0,"AT1G10460.1","GLP7","Germin-like protein subfamily 1 member 1 ","nutrient reservoir activity"]
["isotig15429",99,4.811,19.463,8.934,105.008,81.651,0,0,0,0.807,"AT2G02850.1","ARPN","Basic blue protein ","anther development"]
["isotig28907",99,7.996,39.54,48.229,96.298,98.376,0,0.65,0,1.49,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig16733",99,40.055,75.718,75.983,95.887,16.983,0,0,0,0,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig13103",99,15.678,78.299,95.186,92.194,19.799,0,0,0,1.644,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["PUT-27362",99,63.078,82.033,54.711,88.177,138.384,3.518,3.294,0,7.558,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig59371",99,1.879,25.652,15.096,88.023,87.685,0.367,0,0,0,"AT5G09970.1","CYP78A7","Cytochrome P450 78A7 ","regulation of growth"]
["isotig06047",99,13.133,69.076,67.071,86.496,33.436,0,0.48,0,0,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["PUT-37504",99,65.643,45.648,73.262,86.468,6.632,19.223,3,0,10.323,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["PUT-10584",99,3.541,7.164,17.706,82.632,5.724,2.765,2.589,0,5.94,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig32300",99,0,64.998,43.2,80.615,43.791,3.936,1.843,0,3.17,"AT1G07660.1",null,"Histone H4 ","nucleosome assembly"]
["PUT-21393",99,5.097,25.779,32.768,61.388,16.479,11.941,0,0,4.275,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig37986",99,0,2.369,1.673,59.928,219.548,0,0,0,0,"AT5G59320.1","LTP3","Non-specific lipid-transfer protein 3 ","response to abscisic acid; response to water deprivation"]
["isotig44201",99,182.288,35.528,72.725,56.892,11.859,0,0,0,0.746,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig04574",99,203.454,50.966,34.9,56.315,3.394,0,0,0,0,"AT5G09970.1","CYP78A7","Cytochrome P450 78A7 ","regulation of growth"]
["isotig51521",99,2.105,15.968,13.531,53.075,22.116,1.644,0,0,0,"AT1G09200.1","HTR2","Histone H3.2 ","nucleosome assembly"]
["isotig42131",99,24.325,53.852,47.863,51.129,33.015,0,0.336,0,0,"AT3G07010.1",null,"Probable pectate lyase 8 ","pectin catabolic process"]
["isotig39262",99,4.47,11.755,19.794,50.466,21.676,0.698,0,0,0,"AT5G22880.1","H2B","Histone H2B.10 ","nucleosome assembly"]
["isotig106069",99,6.348,4.28,12.09,49.371,5.13,3.305,1.547,0,0,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig89904",99,12.015,45.912,17.164,46.224,20.501,1.042,0,0,1.12,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]

{"sheet":"Up in M3 (E3SUxM3)","index":7,"n_rows":69,"n_cols":15,"rows_kept":69,"merged":[[3,2,3,6],[3,7,3,10],[37,2,37,6],[37,7,37,10]]}
["Additional file 2: Differentially expressed transcripts (DETs) in embryos and megagametophytes at different stages of seed development. "]
["The Arabidopsis genes showing the highest sequence similarity to the Scots pine transcript are presented (#N/A = no alignment to genes in the TAIR database. Cut off value 1e-5)"]
["The highest up-regulated transcripts in M3/E3SU. Samples subjected to pairwise comparison are highlighted in bold"]
[null,null,"RPKM Embryos ",{"$nulls":4},"RPKM Megagametophytes ",{"$nulls":5},"Arabidopsis homologous gene names and annotation"]
["Transcript ID","Fold change","E1","E2","E3DO","E3SU","E4","M1","M2","M3","M4","At locus ID","At name","At annotation","Involved in"]
["isotig92965",-7.93274444810803,13.921,80.261,22.87,2.096,5.626,213.066,359.304,512.136,388.783,{"$error":"#N/A"}]
["isotig91944",-7.51854741646182,1.396,16.944,1.994,1.051,14.667,105.737,181.68,192.713,270.443,"AT1G03890.1","CRD","12S seed storage protein CRD ","seed maturation; nutrient reservoir activity"]
["isotig96258",-7.48760616330673,1.484,31.527,5.301,1.117,13.196,90.403,219.214,200.469,251.446,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig101116",-6.86419343199273,8.467,8.564,9.676,2.549,1.369,97.854,245.157,296.96,184.628,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig100342",-6.63194347012521,0,20.52,6.038,1.272,8.198,69.968,142.151,126.154,147.455,"AT1G03890.1","CRD","12S seed storage protein CRD ","seed maturation; nutrient reservoir activity"]
["isotig100482",-6.51062380162186,9.993,23.584,8.327,1.254,30.96,100.141,137.604,114.338,209.517,"AT4G28520.2","CRC","12S seed storage protein CRC ","seed maturation; nutrient reservoir activity"]
["isotig101443",-6.49529814749786,6.866,36.459,7.356,1.292,9.711,61.656,138.051,116.558,217.371,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig53419",-6.44691656401336,4.053,5.466,2.895,1.017,2.184,30.597,41.491,88.723,114.446,"AT5G25940.1",null,"early nodulin-related "]
["isotig90894",-6.4131596247139,6.719,4.078,9.599,1.012,6.517,43.027,86.471,86.245,126.235,"AT1G03890.1","CRD","12S seed storage protein CRD ","seed maturation; nutrient reservoir activity"]
["isotig103149",-6.39663272068483,7.327,9.264,10.467,1.379,5.922,52.923,54.911,116.183,35.333,"AT3G15353.1","MT3","metallothionein 3 ","auxin polar transport; response to stress"]
["isotig88106",-6.39647718167345,6.461,13.071,7.384,0.973,1.044,71.648,70.866,81.968,97.542,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig101990",-6.37964992589499,5.34,5.401,7.629,1.34,2.877,75.06,106.723,111.576,116.443,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig85065",-6.3448923569131,3.766,13.967,2.69,0.945,16.234,72.539,89.949,76.813,117.914,"AT5G44120.3","CRA1","12S seed storage protein CRA1 ","seed maturation; nutrient reservoir activity"]
["isotig99643",-6.3278335269598,3.24,39.327,8.1,1.219,17.022,37.951,103.052,97.92,127.715,"AT4G28520.2","CRC","12S seed storage protein CRC ","seed maturation; nutrient reservoir activity"]
["isotig89992",-6.30925801197015,0,25.656,24.793,1.005,20.501,6.255,65.4,79.697,79.495,"AT2G44480.1","BGLU17","Beta-glucosidase 17 ","carbohydrate metabolic process"]
["isotig08295",-6.1958526968352,2.462,4.27,0.503,0.265,2.559,15.383,19.806,19.426,23.308,"AT1G10520.1",null,"DNA polymerase lambda (POLL) ","DNA repair"]
["isotig55129",-6.14888673402957,64.386,164.444,44.84,8.481,137.907,534.216,494.319,601.792,889.651,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig105861",-5.99884811904972,2.094,21.18,23.93,3.152,8.462,89.931,148.508,201.567,184.393,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig93411",-5.98748842215894,2.827,10.008,4.039,1.064,13.71,78.371,62.012,67.508,64.017,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig102309",-5.98727787387205,1.771,26.865,3.794,1.333,32.916,98.17,106.161,84.563,129.195,"AT1G03890.1","CRD","12S seed storage protein CRD ","seed maturation; nutrient reservoir activity"]
["isotig86154",-5.98707127046261,2.507,22.827,4.478,0.944,21.28,60.7,101.754,59.877,125.127,"AT1G03880.1","CRB","12S seed storage protein CRB ","nutrient reservoir activity; response to ABA"]
["isotig92636",-5.98004399307216,5.718,17.352,10.211,3.228,13.865,26.792,106.616,203.754,145.072,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig73754",-5.94235342080638,53.231,7.538,6.844,0.801,0.86,34.917,59.16,49.256,36.608,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig74378",-5.94170077332453,0,8.525,3.01,0.793,5.109,37.02,67.786,48.742,60.082,"AT4G36700.1",null,"RmlC-like cupins superfamily protein ","nutrient reservoir activity"]
["isotig86659",-5.91794771417918,6.316,11.499,3.609,0.951,1.021,72.993,62.804,57.499,37.079,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig101219",-5.8945054148257,3.404,36.152,9.725,2.562,34.39,111.64,150.576,152.406,171.288,"AT1G03880.1","CRB","12S seed storage protein CRB ","nutrient reservoir activity; response to ABA"]
["isotig74564",-5.88375719304294,23.299,106.049,18.911,7.174,28.247,231.558,486.287,423.593,703.451,"AT1G03890.1","CRD","12S seed storage protein CRD ","seed maturation; nutrient reservoir activity"]
["isotig82658",-5.88262967268149,0,31.94,6.073,1.828,13.743,64.492,103.899,107.851,158.9,"AT1G03890.1","CRD","12S seed storage protein CRD ","seed maturation; nutrient reservoir activity"]
["isotig50161",-5.87081273833579,0.988,3.996,2.116,0.743,0,31.618,17.33,43.479,24.847,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig78414",-5.84254854498001,50.745,83.266,49.134,14.43,30.989,353.996,982.007,828.035,1300.413,"AT1G22690.1","GASA9","Gibberellin-regulated protein 9 ","gibberellic acid mediated signaling pathway"]
[]
["The highest up-regulated transcripts in M3 when E3SU RPKM value was equal to 0"]
[null,null,"RPKM Embryos ",{"$nulls":4},"RPKM Megagametophytes ",{"$nulls":5},"Arabidopsis homologous gene names and annotation"]
["ID","Fold change","E1","E2","E3DO","E3SU","E4","M1","M2","M3","M4","At homologous","At Name","At Description","Involved in"]
["isotig107909",-99,14.282,40.931,3.4,0,0,55.764,127.052,310.848,135.751,{"$error":"#N/A"}]
["isotig96968",-99,4.526,7.63,5.388,0,8.535,155.505,167.665,160.985,192.318,{"$error":"#N/A"}]
["isotig110991",-99,0,3.112,0,0,17.409,117.738,119.242,121.697,121.29,{"$error":"#N/A"}]
["isotig106733",-99,2.283,32.335,1.631,0,27.683,108.768,71.791,102.236,151.289,"AT4G28520.2","CRC","12S seed storage protein CRC ","seed maturation; nutrient reservoir activity"]
["isotig114762",-99,0,0,0,0,0,54.087,39.791,95.989,70.538,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig116458",-99,0,6.077,17.164,0,9.711,65.677,70.281,94.143,80.614,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig93604",-99,1.438,8.725,3.081,0,12.782,76.343,83.045,92.265,155.544,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig112237",-99,3.445,3.484,2.46,0,19.489,34.968,50.372,89.966,54.889,"AT1G03890.1","CRD","12S seed storage protein CRD ","seed maturation; nutrient reservoir activity"]
["isotig82478",-99,0,8.62,2.609,0,6.888,51.337,81.005,87.215,106.189,"AT1G03890.1","CRD","12S seed storage protein CRD ","seed maturation; nutrient reservoir activity"]
["isotig101740",-99,5.211,33.384,3.722,0,4.212,29.843,77.478,71.296,90.327,"AT3G22640.1","PAP85","cupin family protein ","response to abiotic stress; nutrient reservoir activity"]
["isotig114480",-99,0,0,3.176,0,3.594,10.416,32.509,69.674,108.137,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig113655",-99,0,20.255,2.861,0,19.422,34.402,38.069,68.739,104.127,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig104923",-99,7.994,4.043,5.71,0,12.923,37.455,54.067,64.129,55.313,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig102531",-99,1.828,11.096,1.306,0,4.433,51.399,56.148,64.126,62.87,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig102395",-99,8.884,16.176,3.808,0,1.436,65.215,68.858,63.646,47.687,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig13374",-99,2.429,2.457,0,0,0,32.246,55.057,62.535,78.432,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig111247",-99,0,0,2.253,0,2.549,27.092,32.285,61.193,31.742,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig112437",-99,3.697,14.958,2.641,0,8.964,28.869,51.359,60.693,49.609,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig102633",-99,0,0,0,0,0,25.333,44.804,60.52,71.041,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig102758",-99,0,20.053,5.149,0,1.457,29.555,52.711,60.52,86.157,"AT3G22640.1","PAP85","cupin family protein ","response to abiotic stress; nutrient reservoir activity"]
["isotig54267",-99,5.176,15.706,1.848,0,4.183,14.146,37.843,59.865,67.282,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig103400",-99,0,0,0,0,0,31.169,48.641,56.734,121.149,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["PUT-30904",-99,8.446,55.528,12.065,0,0,29.678,49.402,53.571,24.791,"ATCG00580.1","PSBE","photosystem II reaction center protein E ","photosynthesis"]
["PUT-17171",-99,66.453,8.402,2.967,0,0,68.11,12.147,52.689,13.933,"AT4G03210.1","XTH9","Xyloglucan endotransglucosylase/hydrolase protein 9 ","cell wall organization"]
["isotig82101",-99,23.775,7.215,4.246,0,5.765,64.981,58.236,52.338,46.859,"AT3G03150.1",0,"unknown"]
["isotig99811",-99,3.325,5.045,4.751,0,13.439,48.041,51.061,52.112,75.302,"AT1G03880.1","CRB","12S seed storage protein CRB ","nutrient reservoir activity; response to ABA"]
["isotig116211",-99,0,11.667,4.119,0,0,31.525,46.385,51.644,62.879,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig99566",-99,3.23,9.8,1.153,0,13.052,26.481,61.397,50.611,44.693,"AT1G03890.1","CRD","12S seed storage protein CRD ","seed maturation; nutrient reservoir activity"]
["isotig100247",-99,0,1.668,1.178,0,1.333,30.907,56.672,50.456,84.368,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig53720",-99,0,5.373,7.588,0,3.22,12.444,35.926,46.576,22.275,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]

{"sheet":"Up in E4 (E4xM4)","index":8,"n_rows":69,"n_cols":15,"rows_kept":69,"merged":[[3,2,3,6],[3,7,3,10]]}
["Additional file 2: Differentially expressed transcripts (DETs) in embryos and megagametophytes at different stages of seed development. "]
["The Arabidopsis genes showing the highest sequence similarity to the Scots pine transcript are presented (#N/A = no alignment to genes in the TAIR database. Cut off value 1e-5)"]
["The highest up-regulated transcripts in E4/M4. Samples subjected to pairwise comparison are highlighted in bold"]
[null,null,"RPKM Embryos ",{"$nulls":4},"RPKM Megagametophytes ",{"$nulls":5},"Arabidopsis homologous gene names and annotation"]
["Transcript ID","Fold change","E1","E2","E3DO","E3SU","E4","M1","M2","M3","M4","At locus ID","At name","At annotation","Involved in"]
["isotig04236",10.0245481714154,32.099,162.718,322.59,587.741,978.037,0.874,0,0,0.939,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig31840",8.26915657962674,0.933,23.587,47.305,59.679,241.252,0.728,0,2.088,0.782,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig101972",7.81108277328173,2337.312,1557.12,774.994,1080.524,331.704,2.751,0,0,1.477,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig03831",7.42973967915391,16.25,111.537,99.077,108.775,83.966,4.985,1.273,3.898,0.487,"AT5G67070.1","RALFL34","Protein RALF-like 34 ","cell-cell signaling; hormone activity"]
["isotig43821",7.26152602423421,5.249,8.343,16.068,21.447,48.18,1.171,1.371,0.28,0.314,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig75051",7.03151085610747,69.346,120.863,172.985,556.51,468.228,5.832,0.78,0,3.579,"AT2G18050.1","HIS1-3","histone H1-3 ","nucleosome assembly"]
["isotig45043",6.98114097274869,7.35,34.85,39.375,43.568,48.64,1.794,1.679,0,0.385,"AT3G54000.1",null,"unknown"]
["isotig55225",6.6748139104656,30.481,190.126,68.945,63.732,145.08,6.612,1.238,1.264,1.42,"ATMG00580.1","NAD4","NADH dehydrogenase subunit 4 ","oxidation-reduction process"]
["isotig15429",6.66075807120997,4.811,19.463,8.934,105.008,81.651,0,0,0,0.807,"AT2G02850.1","ARPN","Basic blue protein ","anther development"]
["isotig46967",6.51692755457852,17.776,79.911,68.657,86.722,50.551,2.571,2.888,3.93,0.552,"AT2G12646.1",null,"PLATZ transcription factor family protein ","unknown"]
["isotig07360",6.4387102249996,71.552,115.799,115.128,326.549,273.941,7.646,0.551,0,3.158,"AT2G18050.1","HIS1-3","histone H1-3 ","nucleosome assembly"]
["isotig51083",6.32148561179495,5.102,6.193,7.289,29.189,68.459,4.781,0.746,1.523,0.856,"AT5G55450.1",null,"Bifunctional inhibitor/lipid-transfer protein","negative regulation of defense response"]
["isotig58592",6.31641971878678,22.081,51.24,46.39,69.092,86.788,1.691,0.633,1.292,1.089,"AT1G72830.1","NFYA3","Nuclear transcription factor Y subunit A-3 ","DNA binding"]
["isotig27987",6.30501971574034,1.055,26.668,35.404,39.691,69.896,0.824,0,0,0.884,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig30508",6.2721861998054,4.571,3.596,9.07,16.44,164.625,1.983,5.571,3.79,2.13,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig82424",6.23212183339301,85.894,179.797,160.199,326.86,451.257,26.085,7.851,7.122,6.003,"AT1G09200.1","HTR2","Histone H3.2 ","nucleosome assembly"]
["isotig80888",6.19108749944424,269.835,417.087,373.798,547.779,787.41,21.892,4.271,2.615,10.777,"ATMG00580.1","NAD4","NADH dehydrogenase subunit 4 ","oxidation-reduction process"]
["isotig83308",6.18056807498442,822.445,673.619,1025.89,1868.158,1106.928,57.783,18.626,9.052,15.261,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig37162",6.1736559651885,0.351,10.66,7.779,6.611,21.295,0.274,0,0.786,0.295,"AT3G24140.1","FAMA","Transcription factor FAMA ","negative regulation of cell division"]
["isotig51059",6.15619512863681,23.714,150.634,119.246,565.477,340.401,12.592,1.387,2.831,4.773,"AT5G59320.1","LTP3","Non-specific lipid-transfer protein 3 ","response to abscisic acid; response to water deprivation"]
["isotig114214",6.15608950982398,650.028,333.077,1020.251,2343.423,1023.125,33.395,18.761,15.956,14.347,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig13900",6.07559893015795,21.662,85.652,37.627,70.039,27.854,3.076,1.08,1.47,0.413,"AT1G08880.1","HTA5","Probable histone H2AXa ","nucleosome assembly"]
["isotig28907",6.04492216000641,7.996,39.54,48.229,96.298,98.376,0,0.65,0,1.49,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig87650",5.99839219747095,7.694,585.015,423.194,1747.17,412.532,7.01,0,0,6.453,"AT5G59320.1","LTP3","Non-specific lipid-transfer protein 3 ","response to abscisic acid; response to water deprivation"]
["isotig113860",5.99100693812194,53.335,336.136,216.855,200.729,437.711,32.038,11.999,3.062,6.882,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig66863",5.94750776880891,35.328,76.341,94.628,90.654,41.533,3.135,0.587,0.599,0.673,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig73073",5.94724485838195,28.689,84.985,87.093,125.714,53.002,1.6,1.498,0,0.859,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig20999",5.6003029222413,21.018,150.313,158.297,123.514,135.012,4.031,4.314,6.329,2.783,"AT5G26340.1","STP13","Sugar transport protein 13 ","transport; response to stress"]
["isotig74937",5.59072929785714,11.963,52.803,59.039,103.146,131.854,4.246,4.771,5.681,2.736,"AT4G32460.1",null,"Protein of unknown function, DUF642 ","unknown"]
["isotig66714",5.56122046184423,12.685,19.246,18.688,28.048,31.399,8.668,0.58,0.592,0.665,"AT3G25980.1","MAD2","Mitotic spindle checkpoint protein MAD2 ","regulation of mitotic cell cycle"]
[]
["Top most up-regulated transcripts in E4 when M4 RPKM value was equal to 0. Pairwise comparison E4 x M4"]
[null,null,"RPKM Embryos ",{"$nulls":4},"RPKM Megagametophytes ",{"$nulls":5},"Arabidopsis homologous gene names and annotation"]
["Transcript ID","Fold change","E1","E2","E3DO","E3SU","E4","M1","M2","M3","M4","At Transcript ID","At Name","At Description","Involved in"]
["isotig37986",99,0,2.369,1.673,59.928,219.548,0,0,0,0,"AT5G59320.1","LTP3","Non-specific lipid-transfer protein 3 ","response to abscisic acid; response to water deprivation"]
["isotig98833",99,980.78,494.428,351.408,472.717,153.43,0,0,1.18,0,"AT5G23870.2","PAE9","Pectin acetylesterase 9 ","cell wall loosening"]
["isotig62874",99,0,9.476,5.353,24.445,139.321,0.488,0,3.262,0,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig21424",99,4.461,4.512,0.797,63.796,130.698,0.871,0,0.832,0,"AT5G59320.1","LTP3","Non-specific lipid-transfer protein 3 ","response to abscisic acid; response to water deprivation"]
["isotig12568",99,0.969,43.128,57.104,27.718,110.827,0,0,0,0,"AT1G77380.1","AAP3","Amino acid permease 3 ","amino acid transmembrane transport"]
["isotig03987",99,1.149,13.945,13.54,31.996,109.105,0,0,0,0,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig25556",99,170.334,77.394,85.883,112.444,92.764,0,0,0,0,"AT1G10460.1","GLP7","Germin-like protein subfamily 1 member 1 ","manganese ion binding; nutrient reservoir activity"]
["isotig59371",99,1.879,25.652,15.096,88.023,87.685,0.367,0,0,0,"AT5G09970.1","CYP78A7","Cytochrome P450 78A7 ","regulation of growth"]
["isotig67423",99,0,2.508,4.723,4.355,62.8,0,0,0,0,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["PUT-24489",99,132.164,93.174,71.517,126.613,61.504,6.255,2.928,2.989,0,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig45589",99,2.49,9.447,5.337,24.37,61.394,2.917,0.91,1.858,0,"AT2G12646.1",0,"PLATZ transcription factor family protein ","unknown"]
["isotig103195",99,0,40.909,64.342,44.28,57.948,0,0,0,0,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["PUT-65564",99,23.38,19.708,50.101,87.994,53.542,9.129,2.849,5.816,0,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig114994",99,0,6.38,0,0,50.983,0,0,0,0,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig60120",99,13.075,26.958,21.192,34.823,50.399,0.785,1.103,0.751,0,"AT1G68810.1","BHLH30","Transcription factor bHLH30 ","regulation of transcription"]
["isotig114306",99,21.658,39.432,12.376,26.083,49.014,27.06,25.337,16.162,0,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig28506",99,2.573,34.484,39.973,58.586,48.351,0.502,0,0.48,0,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig71041",99,0,0,6.233,40.867,47.016,0,0,0,0,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig63058",99,3.16,31.962,29.793,27.114,46.993,0,0,0,0,"AT2G40220.1","ABI4","Ethylene-responsive transcription factor ABI4 ","response to osmotic stress"]
["isotig114701",99,0,0,6.965,7.34,43.348,0,0,0,0,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig85711",99,6.23,17.644,11.57,30.012,40.283,2.919,0.911,0,0,"AT1G09200.1","HTR2","Histone H3.2 ","nucleosome assembly"]
["isotig71508",99,0.985,1.992,1.407,14.823,39.792,0,2.16,2.939,0,"AT2G30420.1","ETC2","MYB-like transcription factor ETC2 ","negative regulation of trichome patterning"]
["isotig81143",99,1.172,0,0,0.882,39.792,0,0,0,0,"AT4G15630.1",0,"CASP-like protein 1E1 ","oxidation-reduction process"]
["isotig53493",99,0,8.497,8.572,14.453,39.768,0,1.755,0,0,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig49361",99,0,0,1.314,5.54,38.667,0,0,0,0,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig69379",99,1.82,18.41,14.301,14.385,38.249,0,0,0,0,"AT2G40260.1",0,"Homeodomain-like superfamily protein ","regulation of transcription"]
["isotig69819",99,0,0.937,15.888,24.416,38.202,0,0,0.692,0,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]
["isotig77461",99,2.221,38.184,33.309,80.23,37.691,5.202,0,1.657,0,"AT3G46940.1","DUT","Deoxyuridine 5'-triphosphate nucleotidohydrolase ","DNA repair"]
["isotig40071",99,9.704,29.737,24.873,15.898,37.372,0,0,0,0,"AT1G51190.1","PLT2","AP2-like ethylene-responsive transcription factor PLT2 ","pattern specification process; stem cell maintenance"]
["isotig87399",99,0,27.171,84.973,25.997,37.22,0,1.871,4.773,0,{"$error":"#N/A"},{"$error":"#N/A"},{"$error":"#N/A"}]

{"sheet":"Up in M4 (E4xM4)","index":9,"n_rows":69,"n_cols":15,"rows_kept":69,"merged":[[3,2,3,6],[3,7,3,10],[37,2,37,6],[37,7,37,10]]}
["Additional file 2: Differentially expressed transcripts (DETs) in embryos and megagametophytes at different stages of seed development. "]
["The Arabidopsis genes showing the highest sequence similarity to the Scots pine transcript are presented (#N/A = no alignment to genes in the TAIR database. Cut off value 1e-5)"]
["The highest up-regulated transcripts in M4/E4. Samples subjected to pairwise comparison are highlighted in bold"]
[null,null,"RPKM Embryos ",{"$nulls":4},"RPKM Megagametophytes ",{"$nulls":5},"Arabidopsis homologous gene names and annotation"]
["Transcript ID","Fold change","E1","E2","E3DO","E3SU","E4","M1","M2","M3","M4","At locus ID","At name","At annotation","Involved in"]
["isotig99197",-7.53687747120351,19.193,72.803,20.564,13.243,1.293,116.158,187.118,193.358,240.118,{"$error":"#N/A"}]
["isotig100129",-7.13003269577195,6.596,35.029,16.491,8.689,1.333,95.296,346.064,292.888,186.717,{"$error":"#N/A"}]
["isotig101116",-7.07535510655197,8.467,8.564,9.676,2.549,1.369,97.854,245.157,296.96,184.628,{"$error":"#N/A"}]
["isotig111359",-6.69697557958693,0,64.816,22.886,33.764,2.59,72.558,203.814,172.147,268.714,{"$error":"#N/A"}]
["isotig88106",-6.54582993665846,6.461,13.071,7.384,0.973,1.044,71.648,70.866,81.968,97.542,{"$error":"#N/A"}]
["isotig75915",-6.35655990247272,0,6.658,6.269,1.651,0.887,5.997,14.438,46.662,72.684,"AT4G11600.1","GPX6","Probable phospholipid hydroperoxide glutathione peroxidase 6, mitochondrial ","response to oxidative stress"]
["isotig77512",-6.22382533206818,22.353,24.871,15.168,25.239,0.903,68.95,71.098,101.753,67.491,{"$error":"#N/A"}]
["isotig77133",-6.20379414554725,5.533,13.432,12.647,19.159,0.894,40.616,78.488,73.497,65.897,{"$error":"#N/A"}]
["isotig92898",-6.16134261419958,4.17,19.686,14.895,6.278,1.124,102.044,68.103,92.327,80.448,{"$error":"#N/A"}]
["isotig98153",-6.15125777393064,29.547,102.243,19.994,23.411,2.514,195.513,200.121,189.156,178.681,{"$error":"#N/A"}]
["isotig92965",-6.110711773885,13.921,80.261,22.87,2.096,5.626,213.066,359.304,512.136,388.783,{"$error":"#N/A"}]
["isotig53589",-6.06456310246723,3.799,19.213,5.427,2.86,2.047,38.566,99.072,98.277,137.004,"AT1G03890.1","CRD","12S seed storage protein CRD ","seed maturation; nutrient reservoir activity"]
["isotig49233",-6.00659476219846,0,3.617,17.24,4.71,0.723,19.546,16.341,30.686,46.484,{"$error":"#N/A"}]
["isotig100247",-5.98394721629086,0,1.668,1.178,0,1.333,30.907,56.672,50.456,84.368,{"$error":"#N/A"}]
["isotig22888",-5.98309479632567,3.134,5.073,5.373,0,0.507,13.217,33.46,26.196,32.07,{"$error":"#N/A"}]
["isotig101416",-5.97934443107203,12.077,87.253,166.361,74.02,20.916,561.792,1190.808,1421.313,1319.595,{"$error":"#N/A"}]
["isotig81911",-5.97469989050283,39.322,55.442,44.258,49.33,4.815,103.284,289.255,352.118,302.803,{"$error":"#N/A"}]
["isotig91688",-5.9600387687385,1.362,2.755,2.919,1.025,1.101,28.717,28.881,44.721,68.539,{"$error":"#N/A"}]
["isotig37510",-5.94885005740747,1.886,13.993,4.941,3.787,1.016,13.749,42.76,43.171,62.759,{"$error":"#N/A"}]
["isotig72490",-5.91196807499758,3.09,3.125,4.414,6.977,0.832,18.497,28.614,32.277,50.096,{"$error":"#N/A"}]
["isotig102758",-5.88589523337827,0,20.053,5.149,0,1.457,29.555,52.711,60.52,86.157,"AT3G22640.1","PAP85","cupin family protein ","response to abiotic stress; nutrient reservoir activity"]
["isotig102265",-5.73981102809209,3.592,29.064,35.917,16.221,8.709,286.081,345.339,438.216,465.397,{"$error":"#N/A"}]
["isotig53419",-5.71155037368439,4.053,5.466,2.895,1.017,2.184,30.597,41.491,88.723,114.446,"AT5G25940.1",null,"early nodulin-related ","response to ethylene"]
["isotig36496",-5.69656131847523,1.249,11.371,3.569,0,1.01,9.754,20.093,42.877,52.379,{"$error":"#N/A"}]
["isotig97313",-5.68735147301498,229.514,648.798,30.399,43.476,3.686,51.038,117.805,115.693,189.941,{"$error":"#N/A"}]
["isotig42503",-5.66914614943463,0,2.856,2.016,1.062,0.38,4.777,14.793,10.533,19.336,"AT5G09220.1","AAP2","Amino acid permease 2 ","acidic amino acid transport"]
["isotig92769",-5.66344696774901,92.885,158.457,199.039,102.265,35.856,859.576,1630.987,1986.307,1817.311,{"$error":"#N/A"}]
["isotig37575",-5.5923818666678,7.751,45.359,13.05,8.334,3.58,70.901,138.036,161.122,172.726,{"$error":"#N/A"}]
["isotig32012",-5.57663694976265,2.006,6.089,3.583,1.51,0.811,23.503,27.875,27.7,38.704,{"$error":"#N/A"}]
["isotig104997",-5.57655154309483,2.035,6.175,0,1.532,1.645,12.712,35.707,31.887,78.501,{"$error":"#N/A"}]
[]
["The hichest up-regulated transcripts in M4 when E4 RPKM value was equal to 0"]
[null,null,"RPKM Embryos ",{"$nulls":4},"RPKM Megagametophytes ",{"$nulls":5},"Arabidopsis homologous gene names and annotation"]
["ID","Fold change","E1","E2","E3DO","E3SU","E4","M1","M2","M3","M4","At homologous","At Name","At Description","Involved in"]
["isotig107909",-99,14.282,40.931,3.4,0,0,55.764,127.052,310.848,135.751,{"$error":"#N/A"}]
["isotig103400",-99,0,0,0,0,0,31.169,48.641,56.734,121.149,{"$error":"#N/A"}]
["isotig13374",-99,2.429,2.457,0,0,0,32.246,55.057,62.535,78.432,{"$error":"#N/A"}]
["isotig13086",-99,11.117,1.606,2.836,4.184,0,34.725,49.932,79.403,73.923,{"$error":"#N/A"}]
["isotig102633",-99,0,0,0,0,0,25.333,44.804,60.52,71.041,{"$error":"#N/A"}]
["isotig114762",-99,0,0,0,0,0,54.087,39.791,95.989,70.538,{"$error":"#N/A"}]
["isotig107511",-99,0,4.672,1.65,1.738,0,30.659,25.33,68.937,67.794,{"$error":"#N/A"}]
["isotig100320",-99,0,10.041,4.727,3.736,0,29.716,91.941,67.906,66.606,"AT3G22640.1","PAP85","cupin family protein","response to abiotic stress; nutrient reservoir activity"]
["isotig74114",-99,4.192,14.841,12.726,6.311,0,46.649,47.511,77.426,65.044,{"$error":"#N/A"}]
["isotig101959",-99,7.145,3.614,7.656,5.378,0,18.134,30.04,19.995,64.42,{"$error":"#N/A"}]
["isotig116211",-99,0,11.667,4.119,0,0,31.525,46.385,51.644,62.879,{"$error":"#N/A"}]
["isotig113022",-99,7.476,7.562,18.69,2.814,0,32.109,57.396,52.999,56.43,{"$error":"#N/A"}]
["isotig104953",-99,21.984,16.172,11.42,1.504,0,26.531,75.987,74.568,55.313,{"$error":"#N/A"}]
["isotig105617",-99,2.103,12.761,3.004,0,0,9.852,33.823,23.536,51.14,{"$error":"#N/A"}]
["isotig76307",-99,15.292,7.734,12.483,8.222,0,34.118,56.704,31.788,50.384,"AT3G52800.1","SAP6","Zinc finger A20 and AN1 domain-containing stress-associated protein 6","response to chitin"]
["isotig102927",-99,7.261,12.853,23.338,38.257,0,22.68,49.108,63.665,50.239,{"$error":"#N/A"}]
["isotig83372",-99,8.451,3.663,5.174,2.726,0,15.084,14.123,40.54,47.588,"AT3G62550.1",null,"Adenine nucleotide alpha hydrolases-like superfamily protein","response to stress"]
["isotig73776",-99,0,9.472,1.486,0,0,8.125,28.149,38.045,45.377,"AT5G18140.1",null,"Chaperone DnaJ-domain superfamily protein "]
["isotig116304",-99,0,0,0,4.495,0,32.644,34.932,31.195,45.077,{"$error":"#N/A"}]
["isotig81319",-99,0,4.821,4.256,3.588,0,36.289,73.185,53.351,43.971,{"$error":"#N/A"}]
["isotig111394",-99,0,0,2.281,0,0,27.435,37.364,45.284,42.858,{"$error":"#N/A"}]
["isotig51777",-99,0,2.195,6.976,5.718,0,12.712,37.294,45.35,42.778,"AT1G63060.1",null,"unknown protein","unknown"]
["isotig106692",-99,8.853,8.955,4.743,1.666,0,10.37,43.694,69.368,42.694,"AT5G25940.1",null,"early nodulin-related","response to ethylene"]
["isotig114674",-99,5.229,0,3.735,7.872,0,16.334,30.589,31.218,39.472,{"$error":"#N/A"}]
["isotig116114",-99,178.782,0,8.239,0,0,63.05,8.434,30.126,38.695,{"$error":"#N/A"}]
["isotig99692",-99,32.4,19.663,16.2,19.51,0,17.711,34.351,42.311,38.043,{"$error":"#N/A"}]
["isotig113695",-99,0,12.25,2.884,3.039,0,31.525,26.566,27.113,37.244,{"$error":"#N/A"}]
["isotig116710",-99,0,0,4.506,0,0,4.926,18.449,9.414,37.032,{"$error":"#N/A"}]
["isotig97158",-99,4.694,3.165,2.235,2.356,0,8.553,35.467,31.527,36.745,{"$error":"#N/A"}]
["isotig70333",-99,1.892,0.957,2.703,0,0,4.432,26.973,12.705,36.492,{"$error":"#N/A"}]