Whole lac-promoter mutagenesis Sort-Seq in E. coli TK310 (0 µM added cAMP)
Using deep sequencing to characterize the biophysical mechanism of a transcriptional regulatory sequenceA partially randomized library spanning the complete 75-nt lac-promoter sequence was assayed in the TK310 background without added cAMP. Reporter fluorescence was measured by FACS and sequence-to-bin assignments were recovered by 454 sequencing across five sorted batches (B1-B5).
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
1 mM IPTG + 0 µM added 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. The TK310 host carries the reported cAMP-pathway/lacY deletions; 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.
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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 · 28 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_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.
- 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.
- total_raw_reads
- Total source sequence records across B1-B5 before duplicate collapse.
- total_deduplicated_observations
- Total retained unique sequence-by-bin observations across B1-B5.
- within_batch_duplicate_reads
- Total source records removed because the same sequence was already observed in that batch.
- bins_observed
- Comma-separated list of sorted batches in which the sequence was observed after deduplication.
- baseline_B0_observed
- Binary indicator for an initial-library B0 observation; always 0 because this condition has no B0 file.
- sorted_bin_observation_count
- Number of retained observations in sorted bins B1-B5.
- activity_bin_mean
- Mean ordinal fluorescence-bin number across retained sorted-bin observations B1-B5.
- activity_bin_median
- Median ordinal fluorescence-bin number across retained sorted-bin observations B1-B5.
- activity_bin_min
- Lowest ordinal fluorescence-bin number observed among B1-B5.
- activity_bin_max
- Highest ordinal fluorescence-bin number observed among B1-B5.
- 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 28,269 resulting unique sequence rows passed these checks. No B0 baseline file is part of this condition; sorted-bin summaries use B1-B5. The table contains 36,798 source records and 28,544 deduplicated sequence-by-bin observations.
Curation notes
This TK310 condition contains five sorted fractions and no B0 baseline in the deposited source. The no-added-cAMP condition may retain low intracellular cAMP from the starter culture, as described by the paper; the perturbation label therefore means 0 µM added cAMP. TK310 is represented with an UNMAPPED biosample CURIE because the requested Cell Ontology/Cellosaurus resolution is not available for this strain. The wild-type sequence used for mutation annotation was resolved from the wt1/wt2 control files.