Library 1 patchMPRA across eight genomic landing pads

A barcoded library of 310 regulatory constructs (282 CRSs plus 28 basal controls), with each CRS represented by 25 distinct CRS barcodes, was integrated by Cre-lox cassette exchange into eight mapped K562 landing-pad clones. The table reports the published log2 RNA/DNA expression measurements for each construct across two biological replicates and eight genomic landing pads, together with prior episomal MPRA expression and ENCODE-derived CRS class.

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

Basal / Untreated

patchMPRA uses a landing-pad cassette with a genomic barcode (gBC) and directional loxFAS/loxP Cre-recombinase cassette exchange. Each integrated reporter contains a CRS barcode (cBC) in the dsRed 3′ UTR, allowing cBC–gBC pairs to identify both regulatory element and genomic location. Library 1 used an Hsp68 minimal promoter, was integrated into eight pooled K562 landing-pad lines, and was measured by matched genomic-DNA and RNA barcode sequencing; the reported activity is log2(RNA reads/DNA reads), averaged over barcode measurements and the two biological replicates.

Quality control

The authors retained barcode pairs only when both cBC and gBC were in the expected sequence context, enriched recombined cells by GFP-loss FACS, and averaged barcode measurements by CRS and landing pad across two biological replicates. They report approximately 11 unique barcode integrations per CRS per landing pad and replicate Spearman correlation Rs = 0.71. For this package, source rows were retained when at least 4 of 8 landing-pad mean-expression values were finite; all 310 source rows passed (282 CRS constructs and 28 basal controls). Missing individual landing-pad measurements are represented as blank fields and were not treated as failed elements.

Curation notes

The paper mapped 15 landing pads overall, but Library 1 pooled LP1–LP8; LP9–LP15 were used for the later library. The source workbook includes 28 Basal control rows without a genomic sequence or coordinate, which are retained because they provide reporter-background measurements. Sequence lengths vary in the source workbook (including short control constructs), so no artificial 130-nt padding was added. This is a non-allelic regulatory-element screen rather than a variant-contrast MPRA; the plasmid_expression column is prior episomal MPRA context from Kwasnieski et al., not a separate experiment performed here.

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

Library 1 patchMPRA across eight genomic landing pads

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