Experiment / E0TF3URP9Sort-Seq / Flow-Seq MPRA

CRP-site mutagenesis Sort-Seq in E. coli MG1655 (500 µM cAMP)

Using deep sequencing to characterize the biophysical mechanism of a transcriptional regulatory sequence

A partially randomized library mutating the CRP-binding portion of the 75-nt lac promoter was assayed in a wild-type E. coli background. Reporter fluorescence was measured by FACS and sequence-to-bin assignments were recovered by 454 sequencing across ten batches (B0-B9).

Download processed table (CSV)Raw source data API documentation

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_MG1655
Reference genome: Not reported / not applicable
Design focus: Synthetic / Motif-focused
Region of interest: Not reported / not applicable

Perturbation & assay details

1 mM IPTG + 500 µM cAMP induction in Vogel Bonner minimal medium with 0.5% glucose at 37 °C

Low-copy pUA66-lacZ-derived plasmid reporters placed the 75-nt lac-promoter sequence upstream of GFP. Cells were sorted into fluorescence bins by FACS, and the promoter insert plus a 7-bp batch barcode were identified by 454 sequencing; the compact source data retain sequence-to-bin observations rather than raw sequence reads.

Processed data

50 rows per page. Click a cell to inspect its full value.

Visible columns (38 of 38)

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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 · 38 definitions

element_id: Experiment-local identifier for a unique 75-nt promoter sequence.
sequence: 75-nt lac-promoter sequence recovered from the reporter amplicon, in the sequenced orientation.
sequence_length: Sequence length in nucleotides; QC requires 75.
mutation_count: Number of positions differing from the wild-type 75-nt lac-promoter reference.
mutated_positions: Comma-separated promoter coordinates from -75 through -1 that differ from the wild-type reference; empty for no differences.
is_wild_type: True if the sequence exactly equals the wild-type 75-nt reference sequence.
raw_reads_B0: Number of source sequence records assigned to initial-library batch B0 before within-batch duplicate collapse.
raw_reads_B1: Number of source sequence records assigned to sorted fluorescence batch B1 before within-batch duplicate collapse.
raw_reads_B2: Number of source sequence records assigned to sorted fluorescence batch B2 before within-batch duplicate collapse.
raw_reads_B3: Number of source sequence records assigned to sorted fluorescence batch B3 before within-batch duplicate collapse.
raw_reads_B4: Number of source sequence records assigned to sorted fluorescence batch B4 before within-batch duplicate collapse.
raw_reads_B5: Number of source sequence records assigned to sorted fluorescence batch B5 before within-batch duplicate collapse.
raw_reads_B6: Number of source sequence records assigned to sorted fluorescence batch B6 before within-batch duplicate collapse.
raw_reads_B7: Number of source sequence records assigned to sorted fluorescence batch B7 before within-batch duplicate collapse.
raw_reads_B8: Number of source sequence records assigned to sorted fluorescence batch B8 before within-batch duplicate collapse.
raw_reads_B9: Number of source sequence records assigned to sorted fluorescence batch B9 before within-batch duplicate collapse.
dedup_observation_B0: Binary presence (0/1) after retaining at most one copy of each sequence in initial-library batch B0.
dedup_observation_B1: Binary presence (0/1) after retaining at most one copy of each sequence in sorted batch B1.
dedup_observation_B2: Binary presence (0/1) after retaining at most one copy of each sequence in sorted batch B2.
dedup_observation_B3: Binary presence (0/1) after retaining at most one copy of each sequence in sorted batch B3.
dedup_observation_B4: Binary presence (0/1) after retaining at most one copy of each sequence in sorted batch B4.
dedup_observation_B5: Binary presence (0/1) after retaining at most one copy of each sequence in sorted batch B5.
dedup_observation_B6: Binary presence (0/1) after retaining at most one copy of each sequence in sorted batch B6.
dedup_observation_B7: Binary presence (0/1) after retaining at most one copy of each sequence in sorted batch B7.
dedup_observation_B8: Binary presence (0/1) after retaining at most one copy of each sequence in sorted batch B8.
dedup_observation_B9: Binary presence (0/1) after retaining at most one copy of each sequence in sorted batch B9.
total_raw_reads: Total source sequence records across B0-B9 before duplicate collapse.
total_deduplicated_observations: Total retained unique sequence-by-bin observations across B0-B9.
within_batch_duplicate_reads: Total source records removed because the same sequence was already observed in that batch.
bins_observed: Comma-separated list of batches in which the sequence was observed after deduplication.
baseline_B0_observed: Binary indicator that the sequence was observed in the initial-library baseline batch B0.
sorted_bin_observation_count: Number of retained observations in sorted bins B1-B9; B0 is excluded.
activity_bin_mean: Mean ordinal fluorescence-bin number across retained sorted-bin observations B1-B9.
activity_bin_median: Median ordinal fluorescence-bin number across retained sorted-bin observations B1-B9.
activity_bin_min: Lowest ordinal fluorescence-bin number observed among B1-B9.
activity_bin_max: Highest ordinal fluorescence-bin number observed among B1-B9.
qc_pass: True for rows passing sequence validity and within-batch duplicate-independence QC.
source_file: Raw-data file from which the sequence/bin observations were taken.

Quality control

The author-filtered sequence/bin files were rechecked for valid batch codes, exactly 75 nt, and only A/C/G/T characters. Repeated observations of the same sequence within a FACS batch were collapsed to one independent sequence-by-bin observation, consistent with the authors' duplicate-sequence QC; all 45,050 resulting unique sequence rows passed these checks. B0 is the random initial-library baseline and is retained as a count column but excluded from activity-bin summaries; sorted-bin summaries use B1-B9. The table contains 62,712 source records and 46,986 deduplicated sequence-by-bin observations.

Curation notes

The library targets the CRP site rather than a natural allele set; the source data are a compact representation of a bacterial Sort-Seq MPRA. The wild-type sequence used for mutation annotation was resolved from the wt1/wt2 control files. Raw duplicate counts are retained for provenance, while activity summaries use deduplicated FACS-bin presence.

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