Experiment / E21HKKTEEStandard STARR-seq

Episomal STARR-seq synthetic TFBS grammar library (10-bp spacer)

Context transcription factors establish cooperative environments and mediate enhancer communication

A synthetic library of 110-bp random-context inserts containing homotypic and heterotypic repeats of eight TF motifs with 10-bp spacers and 12-bp random barcodes was transfected episomally into MEC-1. The table summarizes each sequence construct’s barcode-normalized RNA/DNA activity in two RNA replicates.

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: Human
Taxonomy ID: NCBITaxon:9606
Biosample: CVCL:1870
Reference genome: Not reported / not applicable
Design focus: Synthetic / Motif-focused
Region of interest: Not reported / not applicable

Perturbation & assay details

Basal / Untreated

Episomal hSTARR-ORI-style self-transcribing reporter with the synthetic 10-bp-spacer TF grammar library. The library contains MYC, NFKB, CTCF, PU1, IRF, RUNX3, MEF2, and FOXO motifs; activity is log2 RNA/DNA normalized by the matched no-TFBS context in each replicate. This spacer library was used for the episomal condition only.

Processed data

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

Visible columns (24 of 24)

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 · 24 definitions

element_id: Full identifier for the synthetic sequence construct.
motif_syntax: Base TF motif syntax, excluding the sequence-context suffix.
sequence_context_id: Random sequence-context identifier used to embed the motif syntax.
sequence: Synthetic reporter insert sequence.
spacer_bp: Designed base-pair spacing between adjacent motif instances.
num_of_motifs: Number of TF motif instances in the construct.
homotypic: Whether the construct uses one repeated TF motif rather than a mixed syntax.
tf_first: First TF in the motif syntax.
tf_second: Second TF in the motif syntax when present.
motif_class_composition: Semicolon-delimited context/initiator class labels assigned to the TFs.
n_barcodes_qc: Number of barcode observations retained after plasmid-input and mapping QC.
sum_plasmid_count: Sum of retained barcode plasmid DNA counts.
mean_plasmid_count: Mean retained barcode plasmid DNA count.
sum_mrna_rep1: Sum of retained barcode RNA counts in replicate 1.
sum_mrna_rep2: Sum of retained barcode RNA counts in replicate 2.
mean_mapping_count: Mean source barcode-to-insert mapping count among retained observations.
mean_log2_rna_dna_rep1: Mean unnormalized log2 RNA/DNA activity for replicate 1.
mean_log2_rna_dna_rep2: Mean unnormalized log2 RNA/DNA activity for replicate 2.
mean_log2_activity_norm_rep1: Mean replicate-1 log2 RNA/DNA activity normalized to the matched no-TFBS context.
mean_log2_activity_norm_rep2: Mean replicate-2 log2 RNA/DNA activity normalized to the matched no-TFBS context.
sd_log2_activity_norm_rep1: Standard deviation of barcode-level normalized activity in replicate 1.
sd_log2_activity_norm_rep2: Standard deviation of barcode-level normalized activity in replicate 2.
mean_log2_activity_norm: Mean of the two replicate-level normalized activities.
qc_pass: True for construct rows summarized only from QC-passing barcode observations.

Quality control

Applied the source/paper filter: excluded unmapped or ambiguous barcode assignments and retained only barcodes with plasmid input (plDNA) >=5. All mapped constructs are represented. Output aggregates only retained barcodes; no additional construct-level minimum was imposed.

Curation notes

The table contains 442 synthetic constructs and 210,844 QC-passing barcode observations from 371,944 source count rows. Source normalized activity columns are used and summarized at construct level.

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