Experiment / E8A40B7CAWhole-Genome STARR-seq (WHG-STARR-seq)

HepG2 nonmethylated genomic STARR-seq

Sequence determinants of human gene regulatory elements

Approximately 500-bp sheared human genomic fragments were assayed without exogenous CpG methylation in HepG2 cells using an episomal STARR-seq reporter. This table combines the source MACS2 narrowPeak calls from the two HepG2 biological 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: CVCL:0027
Reference genome: hg19
Design focus: Region-focused
Region of interest: Unbiased whole-genome assay (*)

Perturbation & assay details

Basal / Untreated; nonmethylated genomic library

Unbiased human genomic DNA fragments were cloned into the 3′ UTR of the pCpG-free-Sasaki-SS reporter and measured by STARR-seq in HepG2. The source is the hg19 GSE180152 narrowPeak output for HepG2 NM replicates 1 and 2; methylation was not applied to this library.

Processed data

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

Visible columns (14 of 14)

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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 · 14 definitions

sample_accession: GEO sample accession
replicate: HepG2 replicate or source sample label
chrom: hg19 chromosome
start: Zero-based genomic start coordinate
end: Half-open genomic end coordinate
peak_name: Source peak identifier
score: Source BED/narrowPeak display score
strand: Source strand field
signal_value: MACS2 signal value
neg_log10_p_value: MACS2 -log10 nominal p-value
neg_log10_q_value: MACS2 -log10 q-value
summit_offset: Peak summit offset from start
summit_coordinate: Derived hg19 summit coordinate
peak_length: Derived peak length in bases

Quality control

The source peak files are the paper's MACS2/blacklist-filtered processed outputs. Package QC required integer hg19 coordinates with start < end, valid strands, and finite peak statistics; all 13,790 combined peaks passed and were retained with sample accession and replicate labels.

Curation notes

This experiment combines GSM5454437 (NM1) and GSM5454438 (NM2) while retaining their source labels. The table contains genomic activity peaks, not allele-specific variant effects.

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