Experiment / E9F3A5D10Synthetic Regulatory Grammar MPRA

GP5d TF-motif STARR-seq with CpG-free EF1α reporter

Sequence determinants of human gene regulatory elements

A synthetic transcription-factor motif library containing 43,251 motif patterns in two 49-bp genomic contexts was cloned into the CpG-free EF1α STARR-seq reporter and assayed in GP5d cells. This table contains pattern-level RNA/input activity effects for the E1a reporter condition.

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:1235
Reference genome: hg19
Design focus: Synthetic / Motif-focused
Region of interest: chr10:77103489-77103535,chr8:21525556-21525602

Perturbation & assay details

Basal / Untreated

Episomal self-transcribing active regulatory region sequencing (STARR-seq) in the pCpG-free-EF1α-SS reporter. The synthetic library includes consensus, reverse-complement, degenerate single-base substitutions, repeated copies, and varied orientation/spacing; the source effect is a PsiLFC/log2 RNA-over-input-DNA activity score.

Processed data

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

Visible columns (14 of 14)

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 · 14 definitions

pattern_id: Composite identifier for the motif model, configuration, gap, and sequence context
motif_model: Position-frequency-matrix model name
tf: Transcription-factor label associated with the motif model
reporter_promoter: Reporter promoter condition, E1a here
configuration: Motif orientation/copy configuration reported by GEO
gap: Number of spacer bases between repeated motif copies
sequence_context: Source sequence-context and UMI annotations
context_region_hg19: 49-bp genomic context coordinate from the source
context_gc_rich: Source flag for GC-rich context
umi_length: Length of random UMI bases used in the synthetic oligo
input_count: Input-DNA count for the motif pattern
rna_count: STARR-seq RNA count for the motif pattern
log2_rna_input_effect: Published PsiLFC/log2 RNA-over-input activity effect
source_accession: GEO source accession

Quality control

The paper discarded motif patterns with fewer than 5 combined RNA plus input-DNA counts. Package QC additionally required finite, nonnegative counts and finite effects; 37,615 of 45,524 E1a rows passed and were retained.

Curation notes

The GEO field labels this promoter condition E1a; the vector description identifies the reporter as pCpG-free-EF1α-SS. This is a synthetic motif activity table, not a variant-allele table.

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