A synthetic library combining UP, −35, spacer, −10, and genomic background elements was integrated at the nth-ydgR landing pad using recombination-mediated cassette exchange (RMCE). RNA/DNA barcode sequencing from three biological replicates, including one pair of technical replicates, quantified promoter activity during exponential growth.
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.
Organism
NCBITaxon:511145
Taxonomy ID
NCBITaxon:511145
Biosample
UNMAPPED:Escherichia_coli_K-12_MG1655
Reference genome
U00096.2
Design focus
Synthetic / Motif-focused
Region of interest
Not reported / not applicable
Perturbation & assay details
Basal / Untreated
RMCE cassette integrated at the reverse-orientation nth-ydgR landing pad (rLP5) in E. coli MG1655. Each tested design contains a synthetic promoter, RiboJ insulator, sfGFP reporter, and random 20-nt barcode in the 3′ UTR; the promoter library was measured by RNA and genomic-DNA barcode sequencing. Normalized RNA/DNA counts were aggregated by promoter, with the two technical replicates of biological replicate 1 averaged before combining with biological replicates 2 and 3.
Processed data
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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 · 26 definitions
variant_id
GEO promoter-variant name encoding the UP, −35, spacer, −10, and background design components.
tested_sequence
150-bp perfectly synthesized sequence mapped to the barcode; it contains the designed promoter region, transcription-start nucleotide, and initial transcribed region.
up_element
UP-element identity or noUP label used in the synthetic promoter.
minus35_element
Identity or mutation pattern of the −35 promoter element.
spacer
17-bp spacer sequence/design between the −35 and −10 elements.
minus10_element
Identity or mutation pattern of the −10 promoter element.
background
150-bp E. coli intergenic background identifier used for the promoter design and initial transcribed region.
n_barcodes_mapped
Number of barcode-to-variant associations in the GEO barcode-mapping file for this design.
n_barcodes_counted
Number of mapped barcodes with at least one non-missing normalized DNA or RNA count in the GEO count file.
n_barcodes_with_dna
Number of mapped barcodes with nonzero normalized DNA signal in at least one of the four DNA samples.
n_barcodes_with_rna
Number of mapped barcodes with nonzero normalized RNA signal in at least one of the four RNA samples.
dna_rep1_1_norm_sum
Sum of normalized DNA barcode counts across the design's barcodes for technical replicate 1.1 of biological replicate 1; normalized counts are reads per million.
dna_rep1_2_norm_sum
Sum of normalized DNA barcode counts across the design's barcodes for technical replicate 1.2 of biological replicate 1; normalized counts are reads per million.
rna_rep1_1_norm_sum
Sum of normalized RNA barcode counts across the design's barcodes for technical replicate 1.1 of biological replicate 1; normalized counts are reads per million.
rna_rep1_2_norm_sum
Sum of normalized RNA barcode counts across the design's barcodes for technical replicate 1.2 of biological replicate 1; normalized counts are reads per million.
dna_rep2_norm_sum
Sum of normalized DNA barcode counts across the design's barcodes for biological replicate 2; normalized counts are reads per million.
rna_rep2_norm_sum
Sum of normalized RNA barcode counts across the design's barcodes for biological replicate 2; normalized counts are reads per million.
dna_rep3_norm_sum
Sum of normalized DNA barcode counts across the design's barcodes for biological replicate 3; normalized counts are reads per million.
rna_rep3_norm_sum
Sum of normalized RNA barcode counts across the design's barcodes for biological replicate 3; normalized counts are reads per million.
activity_rep1
RNA/DNA activity ratio for biological replicate 1 after averaging the ratios from technical replicates 1.1 and 1.2.
activity_rep2
RNA/DNA activity ratio for biological replicate 2.
activity_rep3
RNA/DNA activity ratio for biological replicate 3.
activity_rna_dna
Final promoter activity: arithmetic mean of activity_rep1, activity_rep2, and activity_rep3.
log2_activity
Base-2 logarithm of activity_rna_dna.
geo_rna_exp_average
GEO-supplied RNA_exp_average activity value; it matches the reconstructed activity_rna_dna to floating-point precision.
qc_pass
TRUE for a design retained after the package-level barcode-support QC filter; non-passing rows are omitted from table.csv.
Quality control
The authors retained perfectly synthesized promoter matches, required barcode mappings to be consistent within a Levenshtein-distance threshold of 5, and required each barcode to occur at least three times during barcode mapping. They removed promoter designs with fewer than four barcodes detected in either RNA or DNA across the replicates. For this package, the GEO mapping and normalized-count files were joined after normalizing the gourse label spelling; a promoter was retained only when it had at least four mapped barcodes, at least four barcodes with nonzero normalized DNA signal across the four DNA samples, and at least four barcodes with nonzero normalized RNA signal across the four RNA samples. The resulting table contains 10,825 of the 10,898 GEO primary promoter-activity rows; 73 rows were excluded by this explicit barcode-support filter.
Curation notes
The paper's reporter is genomically integrated rather than episomal: a barcoded promoter::RiboJ::sfGFP cassette replaces the nth-ydgR landing-pad cassette in E. coli K-12 MG1655. The public GEO sigma70_variant_data file contains the 10,898 primary promoter designs but not the control rows; the raw barcode mapping also contains negative/positive controls, which are retained only in raw_data and are not part of this primary variant table. GEO mapping names use underscore spellings for gourse UP elements while the variant-activity file uses hyphenated spellings; these labels were normalized only for joining, while variant_id preserves the GEO activity-file spelling. The 150-bp sequence was identical across all barcode mappings for each retained design. The experiment is a single basal condition with three biological replicates; biological replicate 1 has two technical RNA/DNA extraction replicates.