The same 1–1.5 kb size-selected human genomic DNA library was cloned into the ORI-based human STARR-seq vector and electroporated into HeLa-S3 cells without kinase inhibitors. The processed table contains the published genome-wide peak calls from the untreated comparison screen.
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:0058
Reference genome
hg19
Design focus
Region-focused
Region of interest
Unbiased whole-genome assay (*)
Perturbation & assay details
Basal / Untreated (no C16 or BX-795)
Episomal STARR-seq with the bacterial plasmid ORI used as the core promoter; reporter RNA was harvested 6 h after electroporation and sequenced as paired-end 50-cycle reads. Untreated genome-wide reads were mapped as 50-mers, and biological replicates were combined with the corresponding input library for peak calling.
Processed data
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Visible columns (13 of 13)
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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 · 13 definitions
element_id
Published STARR-seq peak identifier (for example, peak_587).
chromosome
Human chromosome name from the hg19-aligned peak call.
start_hg19
Peak start coordinate as reported by the GEO table.
end_hg19
Peak end coordinate as reported by the GEO table.
interval_length_bp
Interval length in base pairs calculated as end - start + 1 from the reported coordinates.
peak_rank
Numeric rank parsed from the published peak identifier.
corrected_enrichment
Peak enrichment over the input library after the paper's correction; retained peaks are at least 4.
p_value
Peak-call p-value reported by GEO; zero denotes numerical underflow in the source result.
chromhmm_state
ChromHMM state overlapping the peak.
genomic_annotation
Genomic feature annotation for the peak, such as intergenic or intronic.
nearest_tss_ensembl75
Ensembl v75 gene identifier for the nearest annotated transcription start site.
nearest_gene
Gene symbol/name associated with the nearest Ensembl v75 transcription start site.
source_table
Filename of the deposited GEO processed table used to create this row.
Quality control
The paper shortlisted STARR-seq-over-input regions at P < 1×10^-5 and enrichment ≥3, called peaks at corrected enrichment ≥4, discarded peaks dominated by a single fragment (>50% of overlapping fragments), and removed peaks overlapping ENCODE blacklist regions. Reads were uniquely mapped to regular human chromosomes 1–22 and X. Package QC additionally required a valid positive-width hg19 interval, a unique peak ID, finite corrected enrichment and p-value, and p-value in [0,1]. All 5,245/5,245 source peak rows passed and no rows were removed; p-value 0 values are retained as reported underflow.
Curation notes
This is the no-inhibitor genome-wide HeLa-S3 screen represented by GSM2683039 and GSM2683040. The untreated screen is retained as a separate condition because plasmid-induced IFN-I signaling is a central biological confounder studied in the paper; the differential comparison is packaged separately.