A 400-bp lentiSTARR-seq library containing candidate cardiac regulatory regions and negative controls was introduced into human iPSC-derived cardiomyocytes at differentiation day 17 and collected at day 24. Six biological DNA and RNA libraries were sequenced to measure enhancer activity as RNA relative to genomic DNA.
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
Region-focused
Region of interest
Not reported / not applicable
Perturbation & assay details
Basal / Untreated
Candidate 400-bp genomic sequences were cloned into the 3′ UTR of a lentiviral self-transcribing reporter, where each enhancer served as its own barcode. The library was delivered to iPSC-CMs during differentiation, and the reporter 3′ UTR was amplified from RNA and genomic DNA seven days later. Activity values in the processed table are the publisher's log2((RNA FPM + 1)/(DNA FPM + 1)) scores for six biological replicates.
Processed data
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Visible columns (42 of 42)
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Filters apply to this table only. The CSV download contains the complete processed table; filtered rows are available through the API.
Column dictionary · 42 definitions
element_id
Unique identifier for the tested 400-bp candidate region.
region_hg19
Candidate region interval on the hg19 assembly.
design_group
Source library design category, such as HHE candidate, noncoding control, or exon control.
nearest_gene
Gene annotation associated with the candidate region in the source workbook.
genomic_location
Source genomic-annotation label for the candidate region.
atac_peak_chr
Chromosome of the iPSC-CM ATAC-seq peak used for candidate selection.
atac_peak_start
Start coordinate of the source ATAC-seq peak.
atac_peak_end
End coordinate of the source ATAC-seq peak.
atac_signal
Source ATAC-seq signal for the selected peak.
dna_count_rep1
Raw genomic-DNA reporter count for replicate 1.
dna_count_rep2
Raw genomic-DNA reporter count for replicate 2.
dna_count_rep3
Raw genomic-DNA reporter count for replicate 3.
dna_count_rep4
Raw genomic-DNA reporter count for replicate 4.
dna_count_rep5
Raw genomic-DNA reporter count for replicate 5.
dna_count_rep6
Raw genomic-DNA reporter count for replicate 6.
rna_count_rep1
Raw reporter-RNA count for replicate 1.
rna_count_rep2
Raw reporter-RNA count for replicate 2.
rna_count_rep3
Raw reporter-RNA count for replicate 3.
rna_count_rep4
Raw reporter-RNA count for replicate 4.
rna_count_rep5
Raw reporter-RNA count for replicate 5.
rna_count_rep6
Raw reporter-RNA count for replicate 6.
dna_fpm_rep1
Publisher-normalized genomic-DNA count in fragments per million for replicate 1.
dna_fpm_rep2
Publisher-normalized genomic-DNA count in fragments per million for replicate 2.
dna_fpm_rep3
Publisher-normalized genomic-DNA count in fragments per million for replicate 3.
dna_fpm_rep4
Publisher-normalized genomic-DNA count in fragments per million for replicate 4.
dna_fpm_rep5
Publisher-normalized genomic-DNA count in fragments per million for replicate 5.
dna_fpm_rep6
Publisher-normalized genomic-DNA count in fragments per million for replicate 6.
rna_fpm_rep1
Publisher-normalized reporter-RNA count in fragments per million for replicate 1.
rna_fpm_rep2
Publisher-normalized reporter-RNA count in fragments per million for replicate 2.
rna_fpm_rep3
Publisher-normalized reporter-RNA count in fragments per million for replicate 3.
rna_fpm_rep4
Publisher-normalized reporter-RNA count in fragments per million for replicate 4.
rna_fpm_rep5
Publisher-normalized reporter-RNA count in fragments per million for replicate 5.
rna_fpm_rep6
Publisher-normalized reporter-RNA count in fragments per million for replicate 6.
log2_activity_rep1
Publisher log2 RNA/DNA enhancer activity score for replicate 1.
log2_activity_rep2
Publisher log2 RNA/DNA enhancer activity score for replicate 2.
log2_activity_rep3
Publisher log2 RNA/DNA enhancer activity score for replicate 3.
log2_activity_rep4
Publisher log2 RNA/DNA enhancer activity score for replicate 4.
log2_activity_rep5
Publisher log2 RNA/DNA enhancer activity score for replicate 5.
log2_activity_rep6
Publisher log2 RNA/DNA enhancer activity score for replicate 6.
mean_log2_activity
Mean publisher enhancer activity score across six replicates.
rank
Rank of the region by publisher mean enhancer activity.
active_enhancer
Publisher DESeq2 activity call: 1 for active/enriched in RNA versus DNA and 0 otherwise.
Quality control
The package retains the publisher's filtered d24 activity sheet: 2,809 of 3,750 designed regions, with complete raw-count and published FPM/activity fields. The paper excluded insufficiently covered regions using an FPM coverage threshold and called active enhancers by DESeq2 RNA-versus-DNA adjusted P < 0.05; the published binary active_enhancer call is preserved. The paper reports highly reproducible six-replicate measurements (Pearson r = 0.95 ± 0.03 across replicates and time points).
Curation notes
The d24 table follows the publisher's filtered activity workbook rather than recomputing DESeq2 calls. Coordinates and annotation fields are reported as hg19, matching the source workbook. The table contains both raw GEO counts and the corresponding publisher-normalized values; no raw-count join was missing.