Whole-genome STARR-seq enhancer activity in CHOK1SV GS-KO cells

A genome-wide episomal STARR-seq plasmid library of randomly sheared CHO genomic DNA fragments (approximately 800 bp) was tested in CHOK1SV GS-KO cells with a core murine CMV promoter. Two biological replicates were harvested 6 h after transfection, and the table contains the authors' final 13,395 RNA-over-input enhancer peak calls with genomic sequences and annotations.

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:10029
Taxonomy ID: NCBITaxon:10029
Biosample: CVCL:DR97
Reference genome: CriGri-PICRH-1.0 (GCF_003668045.3)
Design focus: Region-focused
Region of interest: Unbiased whole-genome assay (*)

Perturbation & assay details

Basal / Untreated (6 h post-transfection)

Episomal plasmid STARR-seq used a synthesized screening vector with a core mCMV promoter upstream of an intron, truncated maxGFP, and the genomic-fragment cloning site. CHO genomic DNA was sonicated and size-selected at approximately 800 bp (700-900 bp); 200 million cells were transfected per screen with 2 micrograms of library and PEI, and RNA was harvested 6 h later. Reporter RNA and plasmid-input libraries were sequenced on an Illumina NextSeq with paired-end 75-cycle reads. Activity is the source STARR-seq RNA/input enrichment and its log2 transform.

Quality control

The authors mapped paired-end input and RNA reads with Bowtie2 v2.5.3, retained properly paired uniquely mapped reads with SAMtools v1.19.1 (view -F 3852 -f 2 -q 40), and normalized genome coverage to RPKM. The two biological replicates correlated at R^2 = 0.94 and were combined. STARRPeaker was run against input; the authors filtered 71,493 candidate calls for p < 1e-5, enrichment over input > 2.5, and regular chromosomes 1-10 and X, yielding the 13,395-row final supplementary Table S3. The packaged table retains every row in that author-supplied final table after validating finite numeric activity fields, valid DNA sequence characters, and unique element IDs.

Curation notes

The source table is the authors' post-filtered final whole-genome STARR-seq enhancer set, not a raw read-level table. Coordinates and chromosome accessions are preserved exactly as supplied; sequence length equals end_position - start_position for these source coordinates. The paper also reports a 6-versus-24 h harvest-time pilot and YY1 motif-mutagenesis STARR-seq, but the supplied supporting files provide those results graphically rather than as machine-readable numeric rows, so they are not represented as additional experiments. The individual GFP/SEAP validation table is retained in raw_data but is not labeled as an MPRA experiment.

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

Whole-genome STARR-seq enhancer activity in CHOK1SV GS-KO cells

Processed data

Quality control

Curation notes

Cite OpenMPRA

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