Sample name	Sample type	Sample subtype	species	ID	AvgSpotLen	BioProject	Reference	LibrarySelection	sex	LibraryLayout	raw read count	trimmed read count	grch38 mapped reads (MAPQ>10)	grch38 %mapped	 mmul10 mapped reads (MAPQ>10)	mmul10 %mapped	RSEM aligned 0 times bowtie2	RSEM aligned 1 time bowtie2	RSEM aligned >1 time bowtie2	RSEM overall alignment rate
H-placenta-021	bulk placenta	H.placenta (DE#1)	Human	SRR12363247	101	PRJNA649979	this study	cDNA (ribo-depleted)	female	SINGLE	41,881,041	41,730,286	30,547,459	73.2%	13,871,379	33.2%	24,093,385	3,659,967	13,976,934	42.3%
H-placenta-044	bulk placenta	H.placenta (DE#1)	Human	SRR12363246	101	PRJNA649979	this study	cDNA (ribo-depleted)	male	SINGLE	68,269,333	68,019,780	42,584,266	62.6%	23,244,722	34.2%	29,522,210	6,747,310	31,750,260	56.6%
H-placenta-077	bulk placenta	H.placenta (DE#1)	Human	SRR12363245	101	PRJNA649979	this study	cDNA (ribo-depleted)	female	SINGLE	70,474,271	70,218,708	49,421,371	70.4%	23,606,003	33.6%	38,687,436	6,295,311	25,235,961	44.9%
H-placenta-123	bulk placenta	H.placenta (DE#1)	Human	SRR12363244	101	PRJNA649979	this study	cDNA (ribo-depleted)	male	SINGLE	51,188,005	51,028,595	32,176,957	63.1%	17,060,972	33.4%	21,316,641	5,535,158	24,176,796	58.2%
H-placenta-160	bulk placenta	H.placenta (DE#1)	Human	SRR12363248	101	PRJNA649979	this study	cDNA (ribo-depleted)	female	SINGLE	36,855,190	36,731,252	24,841,531	67.6%	12,516,990	34.1%	17,556,360	3,752,026	15,422,866	52.2%
H.placenta.SRR3096525	bulk placenta	H.placenta (DE#2)	Human	SRR3096525	250	PRJNA308450	Hydroxymethylation is uniquely distributed within term placenta, and is associated with gene expression	RANDOM	female	PAIRED	91,086,932	88,955,166	42,764,022	48.1%	38,477,816	43.3%	NA	NA	NA	NA
H.placenta.SRR3096545	bulk placenta	H.placenta (DE#2)	Human	SRR3096545	250	PRJNA308450	Hydroxymethylation is uniquely distributed within term placenta, and is associated with gene expression	RANDOM	male	PAIRED	77,146,120	75,517,896	20,416,148	27.0%	44,335,840	58.7%	NA	NA	NA	NA
H.placenta.SRR3096594	bulk placenta	H.placenta (DE#2)	Human	SRR3096594	250	PRJNA308450	Hydroxymethylation is uniquely distributed within term placenta, and is associated with gene expression	RANDOM	male	PAIRED	97,180,406	94,915,508	33,605,579	35.4%	48,136,539	50.7%	NA	NA	NA	NA
H.placenta.SRR3096612	bulk placenta	H.placenta (DE#2)	Human	SRR3096612	250	PRJNA308450	Hydroxymethylation is uniquely distributed within term placenta, and is associated with gene expression	RANDOM	male	PAIRED	96,649,782	94,532,862	33,946,623	35.9%	47,769,751	50.5%	NA	NA	NA	NA
H.placenta.SRR3096624	bulk placenta	H.placenta (DE#2)	Human	SRR3096624	250	PRJNA308450	Hydroxymethylation is uniquely distributed within term placenta, and is associated with gene expression	RANDOM	male	PAIRED	94,364,874	91,989,428	42,697,516	46.4%	37,547,166	40.8%	NA	NA	NA	NA
H.placenta.SRR3096625	bulk placenta	H.placenta (DE#2)	Human	SRR3096625	250	PRJNA308450	Hydroxymethylation is uniquely distributed within term placenta, and is associated with gene expression	RANDOM	female	PAIRED	96,361,426	94,347,814	34,640,974	36.7%	43,632,605	46.2%	NA	NA	NA	NA
H.placenta.SRR4370049	bulk placenta	H.placenta (DE#3)	Human	SRR4370049	100	PRJNA345611	Single-cell transcriptomics of the human placenta: inferring the cell communication network of the maternal-fetal interface	cDNA	undefined	PAIRED	40,873,606	30,294,082	22,397,600	73.9%	12,914,712	42.6%	NA	NA	NA	NA
H.placenta.SRR4370050	bulk placenta	H.placenta (DE#3)	Human	SRR4370050	100	PRJNA345611	Single-cell transcriptomics of the human placenta: inferring the cell communication network of the maternal-fetal interface	cDNA	undefined	PAIRED	35,379,172	28,310,116	19,987,455	70.6%	11,482,497	40.6%	NA	NA	NA	NA
M.placenta.SRR649373	bulk placenta	M.placenta	Mouse	SRR649373	79	PRJNA186646	The evolution of lncRNA repertoires and expression patterns in tetrapods	cDNA	female	SINGLE	26,153,760	23,902,717	NA	NA	NA	NA	4,185,108	5,146,066	14,571,543	82.5%
M.placenta.SRR649374	bulk placenta	M.placenta	Mouse	SRR649374	79	PRJNA186646	The evolution of lncRNA repertoires and expression patterns in tetrapods	cDNA	male	SINGLE	36,618,896	33,775,479	NA	NA	NA	NA	3,620,201	6,047,874	24,107,404	89.3%
M.placenta.SRR943344	bulk placenta	M.placenta	Mouse	SRR943344	101	PRJNA186646	The evolution of lncRNA repertoires and expression patterns in tetrapods	cDNA	pooled male and femal	SINGLE	37,198,366	34,463,049	NA	NA	NA	NA	3,218,268	7,233,245	24,011,536	90.7%
M.placenta.SRR943345	bulk placenta	M.placenta	Mouse	SRR943345	101	PRJNA186646	The evolution of lncRNA repertoires and expression patterns in tetrapods	cDNA	pooled male and femal	SINGLE	31,684,456	29,499,603	NA	NA	NA	NA	3,247,481	6,758,424	19,493,698	89.0%
Rh.placenta.SRR5058999	bulk placenta	Rh.placenta	Rhesus	SRR5058999	150	PRJNA355177	unpublished	cDNA	undefined	PAIRED	25,927,326	21,808,624	7,220,271	33.1%	15,452,393	70.9%	4,298,024	2,382,159	5,108,621	63.5%
Rh.placenta.SRR5059000	bulk placenta	Rh.placenta	Rhesus	SRR5059000	150	PRJNA355177	unpublished	cDNA	undefined	PAIRED	48,361,290	40,253,892	13,007,265	32.3%	28,779,064	71.5%	8,633,558	4,135,126	9,059,218	60.5%
Rh.placenta.SRR7659021	bulk placenta	Rh.placenta	Rhesus	SRR7659021	100	PRJNA485076	Anthropoid primateŠspecific retroviral element THE1B controls expression of CRH in placenta and alters gestation length	cDNA	undefined	PAIRED	45,646,388	36,488,576	12,876,330	35.3%	26,262,040	72.0%	6,823,569	4,044,827	9,229,084	66.1%
Rh.placenta.SRR7659022	bulk placenta	Rh.placenta	Rhesus	SRR7659022	100	PRJNA485076	Anthropoid primateŠspecific retroviral element THE1B controls expression of CRH in placenta and alters gestation length	cDNA	undefined	PAIRED	42,688,486	33,838,900	12,455,351	36.8%	24,468,476	72.3%	5,754,711	4,108,666	8,812,903	69.2%
H.PBMC.SRR3389246	PBMC	H.PBMC	Human	SRR3389246	295	PRJNA316578	Pervasive Inter-Individual Variation in Allele-Specific Expression in Monozygotic Twins	cDNA	male	PAIRED	66,095,663	65,454,088	39,424,855	60.2%	NA	NA	NA	NA	NA	NA
H.PBMC.SRR3390437	PBMC	H.PBMC	Human	SRR3390437	292	PRJNA316578	Pervasive Inter-Individual Variation in Allele-Specific Expression in Monozygotic Twins	cDNA	male	PAIRED	64,752,202	64,130,144	37,598,886	58.6%	NA	NA	NA	NA	NA	NA
H.PBMC.SRR3390461	PBMC	H.PBMC	Human	SRR3390461	295	PRJNA316578	Pervasive Inter-Individual Variation in Allele-Specific Expression in Monozygotic Twins	cDNA	female	PAIRED	52,442,731	51,821,496	31,290,457	60.4%	NA	NA	NA	NA	NA	NA
H.PBMC.SRR3390473	PBMC	H.PBMC	Human	SRR3390473	295	PRJNA316578	Pervasive Inter-Individual Variation in Allele-Specific Expression in Monozygotic Twins	cDNA	female	PAIRED	55,501,807	54,964,798	32,730,525	59.5%	NA	NA	NA	NA	NA	NA
Rh.PBMC.SRR2467156	PBMC	Rh.PBMC	Rhesus	SRR2467156	101	PRJNA296427	Interleukin-21 combined with ART reduces inflammation and viral reservoir in SIV-infected macaques	cDNA	undefined	SINGLE	23,738,749	23,190,380	6,835,837	29.5%	NA	NA	NA	NA	NA	NA
Rh.PBMC.SRR2467157	PBMC	Rh.PBMC	Rhesus	SRR2467157	101	PRJNA296427	Interleukin-21 combined with ART reduces inflammation and viral reservoir in SIV-infected macaques	cDNA	undefined	SINGLE	28,575,830	27,891,854	8,025,745	28.8%	NA	NA	NA	NA	NA	NA
Rh.PBMC.SRR2467159	PBMC	Rh.PBMC	Rhesus	SRR2467159	101	PRJNA296427	Interleukin-21 combined with ART reduces inflammation and viral reservoir in SIV-infected macaques	cDNA	undefined	SINGLE	23,048,129	22,512,897	6,692,994	29.7%	NA	NA	NA	NA	NA	NA
Rh.PBMC.SRR2467160	PBMC	Rh.PBMC	Rhesus	SRR2467160	101	PRJNA296427	Interleukin-21 combined with ART reduces inflammation and viral reservoir in SIV-infected macaques	cDNA	undefined	SINGLE	25,774,753	25,161,441	7,129,306	28.3%	NA	NA	NA	NA	NA	NA
BeWo.SRR6443610	trophoblast	BeWo	Human	SRR6443610	50	PRJNA397241	RNA-Seq identifies genes whose proteins are transformative in the differentiation of cytotrophoblast to syncytiotrophoblast, in human primary villous and BeWo trophoblasts	other	male	SINGLE	98,830,325	94,763,513	51,995,180	54.9%	NA	NA	NA	NA	NA	NA
BeWo.SRR6443613	trophoblast	BeWo	Human	SRR6443613	50	PRJNA397241	RNA-Seq identifies genes whose proteins are transformative in the differentiation of cytotrophoblast to syncytiotrophoblast, in human primary villous and BeWo trophoblasts	other	male	SINGLE	95,999,768	92,445,138	55,919,344	60.5%	NA	NA	NA	NA	NA	NA
BeWo.SRR6443614	trophoblast	BeWo	Human	SRR6443614	50	PRJNA397241	RNA-Seq identifies genes whose proteins are transformative in the differentiation of cytotrophoblast to syncytiotrophoblast, in human primary villous and BeWo trophoblasts	other	male	SINGLE	119,053,899	114,191,668	58,738,816	51.4%	NA	NA	NA	NA	NA	NA
BeWo.SRR6443615	trophoblast	BeWo	Human	SRR6443615	50	PRJNA397241	RNA-Seq identifies genes whose proteins are transformative in the differentiation of cytotrophoblast to syncytiotrophoblast, in human primary villous and BeWo trophoblasts	other	male	SINGLE	107,766,005	103,427,237	69,844,609	67.5%	NA	NA	NA	NA	NA	NA
BeWo.SRR6443616	trophoblast	BeWo	Human	SRR6443616	50	PRJNA397241	RNA-Seq identifies genes whose proteins are transformative in the differentiation of cytotrophoblast to syncytiotrophoblast, in human primary villous and BeWo trophoblasts	other	male	SINGLE	113,732,037	109,520,924	65,345,349	59.7%	NA	NA	NA	NA	NA	NA
BeWo.SRR9118949	trophoblast	BeWo	Human	SRR9118949	150	PRJNA544683	Eutherian-Specific Gene TRIML2 Attenuates Inflammation in the Evolution of Placentation	cDNA	male	PAIRED	43,567,306	42,918,311	25,878,721	60.3%	NA	NA	NA	NA	NA	NA
BeWo.SRR9118950	trophoblast	BeWo	Human	SRR9118950	150	PRJNA544683	Eutherian-Specific Gene TRIML2 Attenuates Inflammation in the Evolution of Placentation	cDNA	male	PAIRED	40,608,391	39,774,909	27,707,804	69.7%	NA	NA	NA	NA	NA	NA
HPT.SRR2397323	trophoblast	HPT	Human	SRR2397323	50	PRJNA296107	Comparison of syncytiotrophoblast generated from human embryonic stem cells and from term placentas	cDNA	female	SINGLE	44,932,439	35,317,215	26,382,058	74.7%	NA	NA	NA	NA	NA	NA
HPT.SRR2397324	trophoblast	HPT	Human	SRR2397324	50	PRJNA296107	Comparison of syncytiotrophoblast generated from human embryonic stem cells and from term placentas	cDNA	female	SINGLE	48,142,481	37,520,054	28,012,877	74.7%	NA	NA	NA	NA	NA	NA
HPT.SRR2397332	trophoblast	HPT	Human	SRR2397332	50	PRJNA296107	Comparison of syncytiotrophoblast generated from human embryonic stem cells and from term placentas	cDNA	male	SINGLE	42,044,005	33,065,909	15,255,075	46.1%	NA	NA	NA	NA	NA	NA
HPT.SRR2397333	trophoblast	HPT	Human	SRR2397333	50	PRJNA296107	Comparison of syncytiotrophoblast generated from human embryonic stem cells and from term placentas	cDNA	male	SINGLE	47,132,098	36,474,549	17,239,762	47.3%	NA	NA	NA	NA	NA	NA
HPT.SRR2397341	trophoblast	HPT	Human	SRR2397341	50	PRJNA296107	Comparison of syncytiotrophoblast generated from human embryonic stem cells and from term placentas	cDNA	male	SINGLE	37,073,520	31,257,099	19,387,931	62.0%	NA	NA	NA	NA	NA	NA
HPT.SRR2397342	trophoblast	HPT	Human	SRR2397342	50	PRJNA296107	Comparison of syncytiotrophoblast generated from human embryonic stem cells and from term placentas	cDNA	male	SINGLE	46,701,841	39,646,408	27,226,488	68.7%	NA	NA	NA	NA	NA	NA
HPT.SRR6443608	trophoblast	HPT	Human	SRR6443608	50	PRJNA397241	RNA-Seq identifies genes whose proteins are transformative in the differentiation of cytotrophoblast to syncytiotrophoblast, in human primary villous and BeWo trophoblasts	other	male	SINGLE	98,786,906	94,635,068	61,370,465	64.8%	NA	NA	NA	NA	NA	NA
HPT.SRR6443609	trophoblast	HPT	Human	SRR6443609	50	PRJNA397241	RNA-Seq identifies genes whose proteins are transformative in the differentiation of cytotrophoblast to syncytiotrophoblast, in human primary villous and BeWo trophoblasts	other	female	SINGLE	103,988,968	98,579,946	61,782,100	62.7%	NA	NA	NA	NA	NA	NA
HPT.SRR6443611	trophoblast	HPT	Human	SRR6443611	50	PRJNA397241	RNA-Seq identifies genes whose proteins are transformative in the differentiation of cytotrophoblast to syncytiotrophoblast, in human primary villous and BeWo trophoblasts	other	male	SINGLE	96,700,936	92,285,479	58,256,446	63.1%	NA	NA	NA	NA	NA	NA
HPT.SRR6443612	trophoblast	HPT	Human	SRR6443612	50	PRJNA397241	RNA-Seq identifies genes whose proteins are transformative in the differentiation of cytotrophoblast to syncytiotrophoblast, in human primary villous and BeWo trophoblasts	other	female	SINGLE	100,646,771	95,485,139	59,556,821	62.4%	NA	NA	NA	NA	NA	NA
iRP-D26-01	trophoblast	iRP	Rhesus	SRR12363173	75	PRJNA649979	this study	cDNA (ribo-depleted)	female	SINGLE	57,819,025	57,300,744	23,404,303	40.8%	36,956,566	64.5%	NA	NA	NA	NA
iRP-D26-02	trophoblast	iRP	Rhesus	SRR12363172	75	PRJNA649979	this study	cDNA (ribo-depleted)	female	SINGLE	64,025,103	63,461,280	26,026,392	41.0%	41,019,351	64.6%	NA	NA	NA	NA
iRP-D28A-01	trophoblast	iRP	Rhesus	SRR12363171	75	PRJNA649979	this study	cDNA (ribo-depleted)	male	SINGLE	68,079,589	67,536,579	27,420,675	40.6%	50,449,368	74.7%	NA	NA	NA	NA
iRP-D28A-02	trophoblast	iRP	Rhesus	SRR12363170	75	PRJNA649979	this study	cDNA (ribo-depleted)	male	SINGLE	68,548,853	67,962,089	25,852,481	38.0%	51,143,453	75.3%	NA	NA	NA	NA
RPT-D50-01	trophoblast	RPT	Rhesus	SRR12363169	75	PRJNA649979	this study	cDNA (ribo-depleted)	male	SINGLE	67,429,414	66,879,283	27,962,950	41.8%	50,695,315	75.8%	NA	NA	NA	NA
RPT-D50-02	trophoblast	RPT	Rhesus	SRR12363168	75	PRJNA649979	this study	cDNA (ribo-depleted)	male	SINGLE	64,225,289	63,635,243	26,493,020	41.6%	46,807,241	73.6%	NA	NA	NA	NA