SOURCE DATA: aTc-IPTG LOW-CROSSTALK SENSOR COMMUNITY

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

Folder / archive
01_aTc_IPTG

Dataset description
This archive contains the experimental plate-reader time courses for the two-member low-crosstalk Escherichia coli sensor community used to detect anhydrotetracycline (aTc) and isopropyl beta-D-thiogalactopyranoside (IPTG). The aTc-responsive strain reports through GFP, and the IPTG-responsive strain reports through mCherry.

The four workbooks collectively contain 326 co-culture time-course samples spanning 80 unique aTc-IPTG input combinations. They also include 48 monoculture control time courses and 9 blank wells. The 326 co-culture samples are the dataset total reported in the manuscript.

Files
1. 2023-03-23 crosstalk plus mixed plate full timecourse.xlsx
   - 68 co-culture samples
   - 24 monoculture controls: 12 aTc-GFP (pLTetO-1) and 12 IPTG-mCherry (T5)
   - 3 blank wells
   - 259 time points, spanning 0-77,398.6 s

2. 2023-03-23 mixed plate full timecourse.xlsx
   - 95 co-culture samples
   - 1 blank well
   - 255 time points, spanning 0-76,200.8 s

3. 2023-03-24 crosstalk plus mixed plate full timecourse.xlsx
   - 68 co-culture samples
   - 24 monoculture controls: 12 aTc-GFP (pLTetO-1) and 12 IPTG-mCherry (T5)
   - 4 blank wells
   - 288 time points, spanning 0-86,100.9 s

4. 2023-03-24 mixed plate full timecourse.xlsx
   - 95 co-culture samples
   - 1 blank well
   - 288 time points, spanning 0-86,097.4 s

Workbook organization
Each workbook contains three worksheets:
- OD: optical-density time courses
- GFP: green-fluorescence time courses
- mCherry: red-fluorescence time courses

The worksheets use the same row ordering within a workbook. Each data row represents one microwell sample. The first four columns contain:
1. Sensor: sample type ("both" for the two-strain co-culture, "pLTetO-1" or "T5" for monoculture controls, and "blank" for media-only wells)
2. aTc: aTc input concentration
3. IPTG: IPTG input concentration
4. Microwell identifier (for example, A1); in the original workbooks this column is labeled "Time [s]"

Columns 5 onward contain measurements at successive time points. Their column headers are elapsed time in seconds. OD values are plate-reader optical-density measurements; GFP 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 2b-f
- Supplementary Figures 1-8
- Supplementary Figure 12a
- Supplementary Figure 13a
- Supplementary Figure 19

Main Figure 2a is a schematic and has no underlying numerical source data. Simulated trajectories, fitted curves, latent-space coordinates, 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. 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 are retained in these files.

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
