SOURCE DATA: VAN-DAPG-NAR THREE-SENSOR COMMUNITY

Paper
Engineering microbial consortia for distributed signal processing
Nature Communications manuscript NCOMMS-26-017824B

Folder / archive
04_Van_DAPG_Nar

Dataset description
This archive contains the experimental plate-reader time courses for the three-member Escherichia coli sensor community used to detect vanillic acid (Van), 2,4-diacetylphloroglucinol (DAPG), and naringenin (Nar). The Van-responsive strain reports through YFP, the DAPG-responsive strain reports through CFP, and the Nar-responsive strain reports through mCherry.

The two workbooks collectively contain 286 co-culture time-course samples spanning 94 unique Van-DAPG-Nar input combinations. The second workbook also contains two blank wells. The 286 co-culture samples are the dataset total reported in the manuscript.

Files
1. 20240531 nar van dapg.xlsx
   - 192 co-culture samples
   - 64 unique Van-DAPG-Nar input combinations
   - 3 replicate wells for every input combination
   - 140 recorded time points, spanning 0-140,588 s

2. 2025-02-21 nar van dapg mixed.xlsx
   - 94 co-culture samples
   - 36 unique Van-DAPG-Nar input combinations
   - 29 input combinations measured in triplicate and 7 mixed-input combinations measured once
   - 2 blank wells
   - 288 recorded time points, spanning 0-86,109.6 s

Six input combinations occur in both workbooks; therefore, the combined dataset contains 94 unique combinations rather than the sum of the workbook-level counts.

Workbook organization
Each workbook contains four worksheets:
- OD: optical-density time courses
- yfp: yellow-fluorescence time courses
- cfp: cyan-fluorescence time courses
- mcherry: red-fluorescence time courses

The four worksheets use identical sample-row ordering and metadata within each workbook. Each data row represents one microwell sample. The first five columns contain:
1. Sensor: sample type ("both" for the three-strain co-culture and "blank" for media-only wells)
2. van: Van input concentration
3. dapg: DAPG input concentration
4. nar: Nar input concentration
5. Plate or microwell identifier; in the original workbooks this column is labeled "Time [s]"

Columns 6 onward contain measurements at successive time points. Their column headers are elapsed time in seconds. OD values are plate-reader optical-density measurements; YFP, CFP, and mCherry values are plate-reader fluorescence measurements. Input-concentration values are preserved exactly as recorded in the experimental workbooks.

Figure mapping
These files provide the experimental source measurements for:
- Main Figure 4c-d
- Supplementary Figure 12d
- Supplementary Figure 13d
- Van-DAPG-Nar entries in Supplementary Table 3

Crosstalk values, fitted dose-response curves, augmented datasets, latent representations, and model predictions shown in these figures are computationally derived from these experimental measurements and can be regenerated using the archived analysis code, fitted parameters, and model files.

Data processing and exclusions
The complete experimental workbooks are supplied here. The two blank wells in the second workbook are retained as controls but are not included in the reported 286-sample co-culture dataset. No co-culture rows in these workbooks are explicitly labeled as contaminated or otherwise excluded.

As described in the Methods, samples with zero inducer concentration or concentrations outside the 1st-99th percentile of the corresponding sensor dynamic range were excluded from specified machine-learning analyses. The unfiltered source measurements, including zero-input conditions used for baseline, crosstalk, and dose-response analyses, are retained in these files.

Plate-reader calibration
Cross-instrument conversion tables used during preprocessing, where applicable, are supplied separately in the 08_Plate_reader_calibration Source Data archive.

Code and reproducibility
Analysis code is available at:
https://github.com/youlab/multiplexed_sensing

The analyses were performed using Python 3.12.7.

Contact
Lingchong You
Department of Biomedical Engineering, Duke University
Email: you@duke.edu
