SOURCE DATA: TTR-THS HIGH-CROSSTALK SENSOR COMMUNITY

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

Folder / archive
02_TTR_THS

Dataset description
This archive contains the experimental plate-reader time courses for the two-member high-crosstalk Escherichia coli sensor community used to detect tetrathionate (TTR) and thiosulfate (THS). The TTR-responsive strain reports through YFP, and the THS-responsive strain reports through CFP.

The three workbooks collectively contain 283 co-culture time-course samples spanning 88 unique TTR-THS input combinations. They also contain four blank wells and one well labeled as contaminated. The contaminated well is retained in the original workbook for transparency but is not included in the 283-sample dataset total reported in the manuscript.

Files
1. 2023-12-04 mixed plate full timecourse_tecanJ_KD.xlsx
   - 94 co-culture samples
   - 47 unique TTR-THS input combinations
   - 2 blank wells
   - 285 time points, spanning 0-85,201.5 s

2. 2024-01-18 ttr ths mixed plate full timecourse_J_plate1.xlsx
   - 94 co-culture samples
   - 64 unique TTR-THS input combinations
   - 1 blank well
   - 1 well labeled as contaminated
   - 288 time points, spanning 0-86,101.5 s

3. 2024-01-18 ttr ths mixed plate full timecourse_loaner_plate2.xlsx
   - 95 co-culture samples
   - 71 unique TTR-THS input combinations
   - 1 blank well
   - 288 time points, spanning 0-86,097.9 s

Some input combinations were measured in more than one workbook; therefore, the sum of the workbook-level unique-combination counts exceeds the 88 unique combinations in the combined dataset.

Workbook organization
Each workbook contains three worksheets:
- OD600: optical-density time courses
- YFP or eYFP: yellow-fluorescence time courses
- CFP: cyan-fluorescence time courses

The worksheets use the same sample-row ordering within each workbook. Each data row represents one microwell sample. The first four columns contain:
1. Sensor: sample type ("both" for the two-strain co-culture, "blank" for media-only wells, or "contaminated" for the excluded well)
2. TTR: tetrathionate input concentration
3. THS: thiosulfate 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. OD600 values are plate-reader optical-density measurements; YFP/eYFP and CFP values are plate-reader fluorescence measurements. Input-concentration values are preserved exactly as recorded in the experimental workbooks.

The raw workbooks contain 285 or 288 time points. During preprocessing, time courses were trimmed and subsampled to a common 285-point representation before kinetic-model fitting and machine-learning analysis, as described in the Methods.

Figure mapping
These files provide the experimental source measurements for:
- Main Figure 3b-d
- Supplementary Figures 9-11
- Supplementary Figure 12b
- Supplementary Figure 13b
- TTR-THS entries in Supplementary Table 3

Main Figure 3a is a schematic and has no underlying numerical source data. Simulated trajectories, fitted dose-response curves, augmented datasets, 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 well explicitly labeled "contaminated" in the second workbook was not included in the reported 283-sample co-culture dataset. 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
These experiments include measurements generated on more than one plate reader. The cross-instrument conversion tables used in preprocessing 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
