Experiment / E9UE9HM3IIntegrated lentiMPRA

Tiling-deletion mutagenesis of human cardiac enhancers

Functional dissection of human cardiac enhancers and noncoding de novo variants in congenital heart disease

The top 123 cardiac enhancers from the cardiac enhancer screen were split into three overlapping 171-bp fragments, and each fragment was tested as a wild-type sequence plus 17 tiled 10-bp deletions. The barcoded lentiviral MPRA library was applied to iPSC-CMs on differentiation day 17 and assayed on day 24 with four biological DNA and RNA replicates.

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: CL:0000746
Reference genome: hg19
Design focus: Variant-focused
Region of interest: Not reported / not applicable

Perturbation & assay details

Basal / Untreated

Each 400-bp enhancer was represented by F1, F2 and F3 171-bp genomic subfragments. Each subfragment and its 10-bp deletion tiles were uniquely barcoded in a lentiviral reporter with the enhancer upstream of a minimal promoter/GFP cassette and the barcode in the reporter 3′ UTR. Reporter RNA and genomic DNA were sequenced after one week in iPSC-CMs; enhancer activity is the publisher's log2 RNA/DNA score.

Processed data

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

Search table valuesFilter columnOperatorValue

Visible columns (59 of 59)

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 · 59 definitions

mutation_pair_id: Stable identifier combining the wild-type and mutant oligo identifiers.
original_400bp_region: Original 400-bp cardiac enhancer interval containing the tested subfragment.
subfragment_coordinates: 171-bp subfragment interval used for the WT and tiled deletion series.
subfragment: Subfragment label F1, F2, or F3.
mutant_tile: Index of the 10-bp deletion tile; 0 is the first deletion and 17 denotes the wild-type reference fragment in the source naming scheme.
wild_type_region: Identifier for the wild-type subfragment oligo.
mutant_region: Identifier for the tiled-deletion oligo.
mean_wt_activity: Publisher mean enhancer activity for the wild-type subfragment.
mean_mut_activity: Publisher mean enhancer activity for the deletion mutant.
log2_foldchange_mut_vs_wt: Publisher log2 activity difference of mutant relative to wild type.
pvalue: Publisher paired-test P value for the WT–mutant comparison.
qvalue: Publisher Benjamini–Hochberg adjusted P value for the WT–mutant comparison.
active_wt: Publisher activity call for the wild-type subfragment: 1 active and 0 inactive.
active_mut: Publisher activity call for the mutant subfragment: 1 active and 0 inactive.
mutation_class_code: Publisher class code: 2 gain of function, 1 loss of function, 0 no change.
mutation_class: Readable mutation class mapped from the publisher code.
mut_median_activity: Publisher median activity reported for the mutant series.
wt_dna_count_rep1: Raw wild-type genomic-DNA reporter count for replicate 1.
wt_dna_count_rep2: Raw wild-type genomic-DNA reporter count for replicate 2.
wt_dna_count_rep3: Raw wild-type genomic-DNA reporter count for replicate 3.
wt_dna_count_rep4: Raw wild-type genomic-DNA reporter count for replicate 4.
wt_rna_count_rep1: Raw wild-type reporter-RNA count for replicate 1.
wt_rna_count_rep2: Raw wild-type reporter-RNA count for replicate 2.
wt_rna_count_rep3: Raw wild-type reporter-RNA count for replicate 3.
wt_rna_count_rep4: Raw wild-type reporter-RNA count for replicate 4.
wt_dna_fpm_rep1: Publisher-normalized wild-type DNA count in fragments per million for replicate 1.
wt_dna_fpm_rep2: Publisher-normalized wild-type DNA count in fragments per million for replicate 2.
wt_dna_fpm_rep3: Publisher-normalized wild-type DNA count in fragments per million for replicate 3.
wt_dna_fpm_rep4: Publisher-normalized wild-type DNA count in fragments per million for replicate 4.
wt_rna_fpm_rep1: Publisher-normalized wild-type RNA count in fragments per million for replicate 1.
wt_rna_fpm_rep2: Publisher-normalized wild-type RNA count in fragments per million for replicate 2.
wt_rna_fpm_rep3: Publisher-normalized wild-type RNA count in fragments per million for replicate 3.
wt_rna_fpm_rep4: Publisher-normalized wild-type RNA count in fragments per million for replicate 4.
wt_log2_activity_rep1: Publisher wild-type log2 RNA/DNA activity score for replicate 1.
wt_log2_activity_rep2: Publisher wild-type log2 RNA/DNA activity score for replicate 2.
wt_log2_activity_rep3: Publisher wild-type log2 RNA/DNA activity score for replicate 3.
wt_log2_activity_rep4: Publisher wild-type log2 RNA/DNA activity score for replicate 4.
wt_mean_log2_activity_published: Publisher mean wild-type log2 RNA/DNA activity score.
mut_dna_count_rep1: Raw mutant genomic-DNA reporter count for replicate 1.
mut_dna_count_rep2: Raw mutant genomic-DNA reporter count for replicate 2.
mut_dna_count_rep3: Raw mutant genomic-DNA reporter count for replicate 3.
mut_dna_count_rep4: Raw mutant genomic-DNA reporter count for replicate 4.
mut_rna_count_rep1: Raw mutant reporter-RNA count for replicate 1.
mut_rna_count_rep2: Raw mutant reporter-RNA count for replicate 2.
mut_rna_count_rep3: Raw mutant reporter-RNA count for replicate 3.
mut_rna_count_rep4: Raw mutant reporter-RNA count for replicate 4.
mut_dna_fpm_rep1: Publisher-normalized mutant DNA count in fragments per million for replicate 1.
mut_dna_fpm_rep2: Publisher-normalized mutant DNA count in fragments per million for replicate 2.
mut_dna_fpm_rep3: Publisher-normalized mutant DNA count in fragments per million for replicate 3.
mut_dna_fpm_rep4: Publisher-normalized mutant DNA count in fragments per million for replicate 4.
mut_rna_fpm_rep1: Publisher-normalized mutant RNA count in fragments per million for replicate 1.
mut_rna_fpm_rep2: Publisher-normalized mutant RNA count in fragments per million for replicate 2.
mut_rna_fpm_rep3: Publisher-normalized mutant RNA count in fragments per million for replicate 3.
mut_rna_fpm_rep4: Publisher-normalized mutant RNA count in fragments per million for replicate 4.
mut_log2_activity_rep1: Publisher mutant log2 RNA/DNA activity score for replicate 1.
mut_log2_activity_rep2: Publisher mutant log2 RNA/DNA activity score for replicate 2.
mut_log2_activity_rep3: Publisher mutant log2 RNA/DNA activity score for replicate 3.
mut_log2_activity_rep4: Publisher mutant log2 RNA/DNA activity score for replicate 4.
mut_mean_log2_activity_published: Publisher mean mutant log2 RNA/DNA activity score.

Quality control

The published raw_values_FPM table retained 7,290 oligo regions after the FPM ≥ 20 DNA-coverage filter, excluding 2.4% of the designed regions. The processed table retains 5,552 WT–mutant comparisons from the publisher's differential-analysis sheet only when both members were present in that coverage-filtered set and had complete raw-count joins. Four independent replicates had Pearson r > 0.9. Published paired-test P values, Benjamini–Hochberg q values, active flags, and mutation classes are preserved; non-significant comparisons are retained as useful negative controls.

Curation notes

This table is deliberately one row per WT–deletion comparison, which is the useful unit for interpreting tiled enhancer mutagenesis. The source workbook does not provide a separate wild-type median for each comparison, so only the reported mutant median is included. Coordinates are reported in hg19 as labeled by the source data.

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