Experiment / E2DIUXO5JEpisomal Plasmid MPRA

CODA candidate CRE episomal MPRA in HepG2

Machine-guided design of cell-type-targeting cis-regulatory elements

The 77,157-oligo CODA library of synthetic candidates, natural human CREs and experimental controls was tested in HepG2 cells using an episomal GFP reporter. The processed table reports HepG2 empirical activity and Malinois predictions after the publication-based reproducibility filter.

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:0027
Reference genome: GRCh38
Design focus: Synthetic / Motif-focused
Region of interest: Not reported / not applicable

Perturbation & assay details

Basal / Untreated

Oligos contained 200-bp inserts upstream of a minimal promoter driving GFP in the pMPRAv3 reporter, with a 20-bp barcode in the GFP 3' UTR. Three biological replicates were performed on different days for each cell type; GFP transcripts were captured and barcode libraries were sequenced on Illumina NovaSeq with 1 x 20-bp chemistry.

Processed data

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

Visible columns (10 of 10)

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 · 10 definitions

element_id: Publication sequence/oligo identifier.
sequence: Tested nucleotide insert sequence; most are 200 bp, while three valid indel controls are 196 or 199 bp.
sequence_origin: Published design or nomination class: AdaLead, DHS_natural, FastSeqProp, Malinois_natural, Simulated_Annealing or control.
target_cell_type: Intended target cell type for designed sequences; empty for controls.
design_round: FastSeqProp motif-penalty round; 0 denotes the unpenalized library or non-penalized classes, and 1-5 denote penalized rounds.
motif_penalty_track: Motif-penalty track identifier for penalized FastSeqProp sequences; empty otherwise.
log2fc: Mean replicate log2 fold-change of reporter expression relative to negative controls in HepG2.
log2fc_se: Standard error across biological replicates for the HepG2 log2 fold-change.
model_prediction_log2fc: Malinois predicted log2 fold-change in HepG2.
min_gap: Published empirical target-cell log2FC minus the maximum off-target log2FC; empty for controls.

Quality control

Applied the publication's stated reproducibility filter and required complete empirical measurements: rows with missing K562, HepG2 or SK-N-SH log2FC/SE values, or with replicate log2FC SE > 1 in any cell type, were excluded. This retained 71,545 of 77,157 source rows, including 1,995 controls; the table's log2FC and SE are the HepG2 fields.

Curation notes

The source library contains 51,000 synthetic candidates, 24,000 natural sequences and 2,157 controls. The same oligo set was assayed in all three cell lines, so the QC filter was applied globally across cell types before selecting the HepG2 measurement. Natural sequences are scattered across the human genome and synthetic sequences have no single genomic locus; the paper states that the reference assembly was GRCh38/hg38.

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