marRAB promoter Sort-Seq — LB medium, Basal / Untreated, E. coli K-12 MG1655 ΔmarRAB, mut2 (4 bins)
Systematic approach for dissecting the molecular mechanisms of transcriptional regulation in bacteriaA continuous mut2 mutagenized window in the marRAB promoter was tested in E. coli K-12 MG1655 ΔmarRAB under LB medium without a stated biological treatment. The table contains author-derived base-resolution expression shifts and mutual-information scores after package QC.
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
Basal / Untreated
Sort-Seq used a mutagenized promoter oligonucleotide library cloned into the low-copy pJK14 (SC101-origin) GFP reporter plasmid. Libraries were grown in the stated medium, sorted by GFP fluorescence on a Beckman Coulter MoFlo XDP, regrown from each sorted bin under kanamycin, and the promoter inserts were amplified for Illumina sequencing. 4 fluorescence bins were used in this run. The standard protocol collected approximately 500,000 cells per bin. The source protocol targeted a 9% mutation rate per nucleotide position for this library. Basal / untreated growth. The deposited summary reports base-resolution effects rather than a conventional RNA/DNA barcode ratio.
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 · 8 definitions
- position
- Source summary position, usually base pairs relative to the native start codon; legacy ns data use a 0-based library position.
- wt_base
- Wild-type nucleotide at the source summary position.
- mutation_rate
- Fraction of sequenced bases at this position that differ from the wild-type nucleotide.
- mutual_information_bits
- Per-position mutual information between nucleotide identity and FACS fluorescence bin, in bits.
- expression_shift_bins
- Mean fluorescence-bin shift caused by mutations at this position; positive values are consistent with loss of repressor binding and negative values with loss of activator/RNAP function.
- expression_shift_3bpavg_bins
- Three-position moving average of the expression shift reported by the authors, in fluorescence-bin units.
- expression_shift_yerr_lower_bins
- Optional lower uncertainty bound for the expression shift in fluorescence-bin units; blank when not present in the source summary.
- expression_shift_yerr_upper_bins
- Optional upper uncertainty bound for the expression shift in fluorescence-bin units; blank when not present in the source summary.
Quality control
The authors retained sequence reads with PHRED >20 at every barcode position and excluded reads missing expected non-mutagenized sequence. Their useful-read yield was generally 300,000–2,000,000 sequences per Sort-Seq experiment. Package QC required a file-level median mutation rate ≥0.01 and then retained rows with integer positions, WT base A/C/G/T, mutation rate ≥0.01, finite mutual information, and finite expression-shift values. Retained 70/70 rows.
Curation notes
Source summary: code/sortseq/20150513_marRmut1only_marRdeltaRAB_marRdeltaR/20150513_marR_MG1655deltamarRAB_LB_na_mut2_4bins_summary.csv. The marRAB library is region-focused and does not encode a specific alternative-allele contrast. This is an MG1655-derived transcription-factor deletion background: MG1655deltamarRAB. The matching repository configuration file is included when available. Positions are kept exactly as supplied by the authors; the configuration files describe them as relative to the native start codon where available. Package QC retained 70 of 70 source rows; 0 rows were removed for missing/zero mutant coverage or non-finite required values.