Experiment / E2TEZ6Y5DSilencer / Repressor MPRA

PMA-differentiated K562 ReSE silencer screen

Systematic identification of silencers in human cells

The same approximately 200-bp K562 FAIRE-enriched ReSE library was assayed after K562 cells were differentiated with PMA. AP20187-selected survivors were compared with PMA-treated untreated controls in two biological replicates, and the table contains the published significantly enriched silencer fragments.

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:0004
Reference genome: hg19
Design focus: Region-focused
Region of interest: Not reported / not applicable

Perturbation & assay details

10 nM PMA for 2 days, then 1 nM AP20187 for 18 h; apoptotic cells removed, surviving cells expanded for 5 days (versus PMA-treated untreated control)

The integrated ReSE lentiviral reporter library was tested in PMA-differentiated K562 cells. After PMA treatment, AP20187 activated FKBP-Casp9 in cells not protected by a repressive insert; surviving inserts were sequenced and analyzed against PMA-treated controls using the same Bowtie/hg19, HTSeq, median-normalization, and MAGeCK framework as the parental K562 screen.

Processed data

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

Visible columns (7 of 7)

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 · 7 definitions

element_id: ReSE fragment identifier from the published ID field.
chrom: Chromosome for the tested fragment in hg19.
start: 0-based inclusive fragment start coordinate, matching the GEO BED file.
end: 0-based exclusive fragment end coordinate, matching the GEO BED file.
length_bp: Fragment length in base pairs, calculated as end minus start.
fdr: MAGeCK/BH false-discovery rate for enrichment after AP20187 selection in PMA-treated K562 cells versus PMA-treated untreated control.
fold_enrichment: Published semi-quantitative fold change/enrichment for the post-selection fragment abundance.

Quality control

The authors used two biological replicates, Bowtie alignment to hg19, a quality ≥30 read-count filter, median normalization for library size and count distributions, and MAGeCK negative-binomial testing with Benjamini–Hochberg FDR. Fragments with FDR < 0.01 were retained as significant hits. Package QC additionally required a valid hg19 chromosome, nonnegative start, end > start, unique element ID, finite FDR in [0, 0.01), and finite positive fold enrichment; the Supplementary Table and matching GEO BED file agreed for all 1,341 retained rows, so no source rows were removed.

Curation notes

This is a pooled integrated lentiviral ReSE survival screen in PMA-differentiated K562 cells. The paper's main text states 1,245 PMA-associated silencers, whereas the deposited Supplementary Table 2 and matching GEO BED contain 1,341 FDR < 0.01 rows; the deposited files were used for the processed table. K-562 was resolved to Cellosaurus CVCL:0004.

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