Genome-integrated Reg-Seq MPRA across 39 E. coli environments
Illuminating the uncharacterized regulatory genome of E. coli with massively parallel reportersA pooled library of 178,619 designed variants covering 119 promoter constructs was mutagenized across 160 bp windows, linked to 20 bp barcodes, and integrated into the E. coli chromosome. DNA and cDNA barcode sequencing was performed for 39 growth conditions in two or three biological replicates; this package aggregates the authors' 88 paired processed condition-replicate summaries into one position-by-condition table.
Processed tables are specific to each experiment. Column names, units, measurements, and table structure are not standardized across the database. Check this experiment’s column definitions and quality-control notes before comparing or combining data.
Perturbation & assay details
Condition-specific media, nutrient, osmotic, temperature, redox, antibiotic, and chemical stress treatments across 39 environments; exact conditions are in raw_data/condition_manifest.csv and the condition column of table.csv.
The library was assembled with a RiboJ::sfGFP reporter and a 20 bp barcode, then integrated into an attB landing pad near glmS using the ORBIT attB/attP recombination system. Genomic DNA barcode counts estimate the abundance of each promoter variant and cDNA barcode counts estimate reporter transcription; the released summaries contain mutual-information footprints and signed per-base expression-shift matrices. The GFP cassette carried a premature stop codon, so fluorescence was not used; all comparisons are based on the mRNA-to-DNA barcode ratio. Promoter positions span -115 to +44 relative to each transcription start site. Sequencing used MiSeq or NextSeq 2000 runs listed in raw_data/sra_runinfo.csv.
Processed data
50 rows per page. Click a cell to inspect its full value.
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Filters apply to this table only. The CSV download contains the complete processed table; filtered rows are available through the API.
Column dictionary · 17 definitions
- condition_index
- Author-assigned numeric condition/file prefix, preserving the link to the per-replicate raw files.
- condition
- Cleaned condition name mapped from the authors' growth-condition metadata.
- promoter
- Unique promoter construct identifier.
- genes
- Gene or genes associated with the promoter, from the authors' promoter metadata.
- position_relative_to_tss
- Mutagenized position relative to the promoter transcription start site, from -115 to +44.
- wt_base
- Wild-type nucleotide at the position.
- mean_expression_shift_A
- Mean signed expression shift for variants carrying an A at the position, across biological replicates; the authors' base index 1.
- mean_expression_shift_C
- Mean signed expression shift for variants carrying a C at the position, across biological replicates; the authors' base index 2.
- mean_expression_shift_G
- Mean signed expression shift for variants carrying a G at the position, across biological replicates; the authors' base index 3.
- mean_expression_shift_T
- Mean signed expression shift for variants carrying a T at the position, across biological replicates; the authors' base index 4.
- sd_expression_shift_A
- Sample standard deviation of the A expression shift across biological replicates.
- sd_expression_shift_C
- Sample standard deviation of the C expression shift across biological replicates.
- sd_expression_shift_G
- Sample standard deviation of the G expression shift across biological replicates.
- sd_expression_shift_T
- Sample standard deviation of the T expression shift across biological replicates.
- mean_mutual_information_bits
- Mean per-position mutual information between mutation state and DNA-versus-RNA barcode readout, in bits, across biological replicates.
- sd_mutual_information_bits
- Sample standard deviation of per-position mutual information across biological replicates.
- replicate_count
- Number of paired biological condition replicates contributing to the row.
Quality control
The authors filtered and merged barcode-mapping reads with fastp and custom scripts, discarded promoter-variant/barcode pairs with fewer than 3 total reads, and retained variants associated with at least 2 barcodes for the library QC (172,418 recovered variants, containing more than 96.5% of the 178,619 designed variants). Conditions were run in duplicate, with a third replicate when initial mutual-information footprints did not correlate well. Package QC retained only finite, complete promoter-position records having paired footprint and expression-shift values in every available condition replicate (at least 2) and all four nucleotide bins; incomplete keys were excluded from table.csv. The original per-replicate summary files remain in raw_data.
Curation notes
The released repository contains 88 paired processed condition-replicate summaries for the 39 conditions, while SRA run metadata also lists an additional 20-3 DNA/RNA pair and the separate barcode-mapping run; no processed 20-3 summary was available, so it is not fabricated into table.csv. The processed nucleotide columns map the repository's explicit encoding A=1, C=2, G=3, T=4. The current promoter metadata contains 119 promoter records, whereas the released footprint/expression-shift summaries cover 114 promoter IDs; original design and wild-type sequence files are retained under raw_data/metadata.