HeLa-S3 whole-genome ORI STARR-seq with TBK1/IKK and PKR inhibition
Resolving systematic errors in widely-used enhancer activity assays in human cells enables genome-wide functional enhancer characterizationA genome-wide library of 1–1.5 kb size-selected human genomic DNA fragments was cloned into the ORI-based human STARR-seq vector and electroporated into HeLa-S3 cells. Cells received 1 µM PKR inhibitor C16 and 1 µM TBK1/IKK inhibitor BX-795 immediately after electroporation; the processed table contains the published peak calls from the inhibitor 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.
Perturbation & assay details
1 µM PKR inhibitor C16 + 1 µM TBK1/IKK inhibitor BX-795 added immediately after electroporation
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. Inhibitor-screen reads were mapped as 36-mers, and biological replicates were combined with the corresponding input library for peak calling.
Processed data
50 rows per page. Click a cell to inspect its full value.
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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 · 16 definitions
- element_id
- Published STARR-seq peak identifier (for example, peak_7597).
- 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.
- hela_s3_dhs_significant
- 1 if the peak had significant HeLa-S3 DHS enrichment in the published annotation, otherwise 0.
- other_dhs_significant
- 1 if the peak had significant DHS enrichment in other cell types in the published annotation, otherwise 0.
- enriched_transposable_element
- 1 if the peak was annotated as enriched for a transposable element, otherwise 0.
- 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 9,613/9,613 source peak rows passed and no rows were removed; p-value 0 values are retained as reported underflow.
Curation notes
This is the inhibitor-treated genome-wide HeLa-S3 screen represented by GSM2683035 and GSM2683036, with ORI_geomewide_input_lib1/2 as input-library controls. The table is a peak-level enhancer activity resource rather than a barcode-level count matrix or an allele-contrast dataset. Coordinates and Ensembl annotations follow the study's hg19/Ensembl v75 processing; the preliminary 71,968-row shortlisted-region file is retained in raw_data but was not substituted for the final corrected-enrichment ≥4 peak calls.