Experiment / E93NV7EQWSort-Seq / Flow-Seq MPRA

Whole lac-promoter mutagenesis Sort-Seq in E. coli TK310 (500 µM cAMP)

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

A partially randomized library spanning the complete 75-nt lac-promoter sequence was assayed in the TK310 background with exogenous cAMP. Reporter fluorescence was measured by FACS and sequence-to-bin assignments were recovered by 454 sequencing across five sorted batches (B1-B5).

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_TK310
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. 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.

Visible columns (28 of 28)

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

Page 1 · 50 rows · More results available

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 23,251 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 29,810 source records and 23,431 deduplicated sequence-by-bin observations.

Curation notes

This TK310 condition contains five sorted fractions and no B0 baseline in the deposited source. TK310 is represented with an UNMAPPED biosample CURIE because the requested Cell Ontology/Cellosaurus resolution is not available for this strain; the paper describes it as a cAMP-pathway/lacY deletion background. The wild-type sequence used for mutation annotation was resolved from the wt1/wt2 control files.

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

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

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