Combinatorial promoter–RBS FlowSeq MPRA in Escherichia coli MG1655
Composability of regulatory sequences controlling transcription and translation in Escherichia coliAn episomal pGERC reporter library combined 114 promoters with 111 ribosome-binding sites upstream of superfolder GFP, with constitutive mCherry as an internal control. DNA-seq and RNA-seq quantified construct representation and transcript abundance, while FlowSeq measured GFP/RFP protein output across twelve FACS bins during basal growth of E. coli MG1655.
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
The low-copy episomal pGERC plasmid placed each promoter–RBS combination upstream of superfolder GFP and expressed mCherry from a constitutive PLtetO-1 control promoter. The primary library was assayed by two technical DNA-seq replicates, two technical RNA-seq replicates, and 12-bin GFP/RFP FlowSeq; the processed table contains the primary-library counts and excludes the separate 42-clone spike-in measurements. RNA activity is the authors' normalized RNA/DNA ratio, protein activity is the authors' calibrated GFP/RFP FlowSeq level, and promoter sequences retain the authors' five-base barcode used for transcription-start-site identification.
Processed data
50 rows per page. Click a cell to inspect its full value.
Visible columns (50 of 50)
| Row | ||||||||||||||||||||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 2 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 3 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 4 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 5 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 6 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 7 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 8 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 9 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 10 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 11 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 12 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 13 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 14 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 15 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 16 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 17 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 18 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 19 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 20 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 21 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 22 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 23 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 24 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 25 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 26 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 27 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 28 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 29 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 30 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 31 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 32 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 33 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 34 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 35 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 36 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 37 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 38 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 39 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 40 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 41 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 42 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 43 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 44 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 45 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 46 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 47 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 48 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 49 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 50 |
Filters apply to this table only. The CSV download contains the complete processed table; filtered rows are available through the API.
Column dictionary · 50 definitions
- construct_id
- Authors' full promoter--RBS construct identifier.
- promoter_id
- Canonical Ec-TTL-P### promoter identifier from Dataset S1/S3.
- promoter_name
- Source or library name of the promoter element.
- promoter_num
- Authors' numeric promoter order in the transcription/translation library.
- promoter_sequence
- Uppercase promoter-library sequence from Dataset S1, including the AscI cut site, promoter sequence, and terminal five-base TSS barcode; spaces were removed.
- promoter_sequence_length_bp
- Length of promoter_sequence in base pairs.
- promoter_barcode_5nt
- The terminal five nucleotides of promoter_sequence, used by the authors for transcription-start-site identification.
- promoter_tss_relative_to_junction
- Most prevalent transcription-start-site position relative to the promoter/RBS junction.
- promoter_tss_fraction
- Fraction of mapped RNA contigs beginning at the dominant promoter transcription-start site.
- rbs_id
- Canonical Ec-TTL-R### RBS identifier from Dataset S2/S3.
- rbs_name
- Source or library name of the RBS element.
- rbs_num
- Authors' numeric RBS order in the transcription/translation library.
- rbs_sequence
- Uppercase RBS-library sequence from Dataset S2, including the terminal CATATG cloning/start-codon context; spaces were removed.
- rbs_sequence_length_bp
- Length of rbs_sequence in base pairs.
- dna_count_rep_a
- Primary-library DNA-seq construct count in technical replicate A.
- dna_count_rep_b
- Primary-library DNA-seq construct count in technical replicate B.
- dna_count_total
- Total primary-library DNA-seq construct count across replicates as reported in Dataset S3.
- rna_count_rep_a
- Primary-library RNA-seq construct count in technical replicate A.
- rna_count_rep_b
- Primary-library RNA-seq construct count in technical replicate B.
- rna_count_total
- Total primary-library RNA-seq construct count across replicates as reported in Dataset S3.
- rna_activity_rep_a
- Normalized RNA/DNA activity ratio for technical replicate A.
- rna_activity_rep_b
- Normalized RNA/DNA activity ratio for technical replicate B.
- rna_activity_mean
- Mean normalized RNA/DNA activity across the two technical replicates; the paper's RNA level.
- flowseq_count_total
- Total primary-library FlowSeq contig count across all twelve bins.
- flowseq_bin_1
- Primary-library FlowSeq contig count in FACS bin 1.
- flowseq_bin_2
- Primary-library FlowSeq contig count in FACS bin 2.
- flowseq_bin_3
- Primary-library FlowSeq contig count in FACS bin 3.
- flowseq_bin_4
- Primary-library FlowSeq contig count in FACS bin 4.
- flowseq_bin_5
- Primary-library FlowSeq contig count in FACS bin 5.
- flowseq_bin_6
- Primary-library FlowSeq contig count in FACS bin 6.
- flowseq_bin_7
- Primary-library FlowSeq contig count in FACS bin 7.
- flowseq_bin_8
- Primary-library FlowSeq contig count in FACS bin 8.
- flowseq_bin_9
- Primary-library FlowSeq contig count in FACS bin 9.
- flowseq_bin_10
- Primary-library FlowSeq contig count in FACS bin 10.
- flowseq_bin_11
- Primary-library FlowSeq contig count in FACS bin 11.
- flowseq_bin_12
- Primary-library FlowSeq contig count in FACS bin 12.
- protein_activity_gfp_rfp
- Authors' calibrated FlowSeq protein activity in GFP/RFP relative fluorescence units.
- translation_efficiency_protein_per_rna
- Derived protein_activity_gfp_rfp divided by rna_activity_mean; a construct-level proxy for translation efficiency.
- deltaG_5prime_utr_kcal_mol
- Predicted RNA secondary-structure free energy for the sequence from the dominant TSS through 30 bases of sfGFP, in kcal/mol.
- promoter_mean_rna_activity
- Geometric mean RNA activity across constructs carrying this promoter, as reported in Dataset S3.
- promoter_mean_protein_activity
- Geometric mean protein activity across constructs carrying this promoter, as reported in Dataset S3.
- rbs_mean_rna_activity
- Geometric mean RNA activity across constructs carrying this RBS, as reported in Dataset S3.
- rbs_mean_translation_efficiency
- Geometric mean protein/RNA translation efficiency across constructs carrying this RBS, as reported in Dataset S3.
- model_rna_activity_simple
- RNA activity predicted by the paper's simple promoter-mean model.
- model_protein_activity_simple
- Protein activity predicted by the paper's simple promoter-mean times RBS-translation model.
- model_protein_activity_anova
- Protein activity predicted by the paper's promoter-plus-RBS ANOVA model.
- model_rna_activity_anova
- RNA activity predicted by the paper's promoter-plus-RBS ANOVA model.
- rna_fold_vs_simple_model
- Derived observed rna_activity_mean divided by model_rna_activity_simple.
- protein_fold_vs_simple_model
- Derived observed protein_activity_gfp_rfp divided by model_protein_activity_simple.
- qc_pass
- TRUE for every retained row after the documented paper-based and conservative low-RNA QC filters.
Quality control
Applied the authors' SI QC criteria: unique/perfect construct mapping for FlowSeq contigs with at least 100 occurrences across multiple bins (except the final bin), at least 10 DNA contig counts in each DNA replicate, and the authors' RNA/DNA count filters; late-transcription-start-site promoters were excluded by the bad.promo flag. Rows were retained only when bad.prot, bad.DNA, bad.RNA, bad.promo, min.prot, and max.prot were all FALSE. As a conservative additional filter, the 12 rows with min.RNA=TRUE were removed because the authors imputed their low RNA counts to 10 for calculation. This retains 9,336 of 12,655 source Dataset S3 rows; all retained rows have measured RNA counts of at least 20 in both technical replicates and protein values inside the reported FlowSeq linear range.
Curation notes
This is an early bacterial multiplexed reporter assay rather than an allele-contrast MPRA: the library tests combinatorial compatibility of common promoters and RBSs. The source Dataset S3 contains 12,655 rows, including late-TSS/invalid construct rows and measurements outside the FlowSeq linear range; the processed table intentionally retains only the 9,336 rows passing the stated filters. Reference genome and genomic region are null because the tested sequences are synthetic/library elements rather than genomic loci. The biosample is left UNMAPPED because the supplied biosample CURIE rules cover eukaryotic cell lines, primary cells, tissues, and organs rather than bacterial culture strains.