Experiment / E5H5D9H9STargeted / Cap-STARR-seq

CapSTARR-seq — GM12878 untreated

Comprehensive mapping of genetic variation at Epromoters reveals pleiotropic association with multiple disease traits

Targeted CapSTARR-seq of a human reference-sequence promoter library in GM12878 under Basal / Untreated. The table retains promoter elements called Active in every available biological replicate and aggregates their GEO-processed FPKM and fold-change values.

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:7526
Reference genome: hg19
Design focus: Region-focused
Region of interest: Not reported / not applicable

Perturbation & assay details

Basal / Untreated

Episomal CapSTARR-seq using a captured human promoter library. GEO processed VS_input tables provide normalized FPKM, input FPKM, fold_change, and the ranked fold-change inflection-point activity call; raw sequencing reads are intentionally not included.

Processed data

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

Visible columns (14 of 14)

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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 · 14 definitions

element_id: Stable interval identifier in chr:start-end format.
chr: Chromosome from the GEO processed CapSTARR-seq table.
start: Zero-based or source-convention start coordinate from GEO processed data.
end: End coordinate from GEO processed data.
category: Source library category, typically hPro for human promoter fragments.
gene_name: Gene name(s) associated with the promoter fragment in GEO.
replicate_count: Number of biological replicate VS_input files aggregated.
active_replicates: Number of replicates with the source inflection-point Active call; retained rows equal replicate_count.
replicate_accessions: GEO sample accessions contributing to the aggregate row.
mean_fpkm: Arithmetic mean of normalized CapSTARR-seq FPKM across replicates.
mean_fpkm_input: Arithmetic mean of normalized input-library FPKM across replicates.
mean_fold_change: Arithmetic mean of CapSTARR-seq FPKM divided by input FPKM across replicates, using source fold_change values.
log2_activity: Log2 of mean_fold_change; a compact activity score, not an allelic effect.
activity_call: Active because the element passed the source ranked fold-change inflection-point call in every replicate.

Quality control

The paper removed promoter regions with input FPKM < 1 and called enhancer activity using the inflection point of ranked fold-change. This package additionally retained only elements marked Active in every available biological replicate, required fpkm_input >= 1 in every replicate, excluded non-finite values, and averaged replicate values. The GEO source files had no input-FPKM failures among their rows.

Curation notes

Source GEO accession GSE268615; processed files retained under raw_data/geo_GSE268615. Replicate files: GSM8295419_CapSTARR-seq_GM12878_WT_rep1_VS_input.tsv.gz; GSM8295420_CapSTARR-seq_GM12878_WT_rep2_VS_input.tsv.gz; GSM8295421_CapSTARR-seq_GM12878_WT_rep3_VS_input.tsv.gz. The paper mapped these processed CapSTARR fragments to hg19 and later converted its merged enhancer collection to hg38. Supplemental Table 3 is retained as raw material but is not joined here across assemblies.

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