Population STARR-seq at the fetal-adiposity locus in HepG2
Bayesian estimation of genetic regulatory effects in high-throughput reporter assaysThe public GSE77743 population STARR-seq assay captured regulatory fragments from 104 DHS regions at the chromosome 3q25 fetal-adiposity locus in 760 donors and transfected the pooled library into HepG2 cells. The processed table preserves the official haplotype-level effect release and adds signed log2 effect and an FDR convenience flag.
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
Basal / Untreated
Population STARR-seq (POP-STARR) used multiplex PCR capture of donor genomic fragments, cloned the fragments into the 3' UTR of a self-transcribing reporter, and measured reporter RNA relative to plasmid input after approximately 48 hours in three HepG2 transfections. The public haplotype-effects file is an official effect-level release and does not contain the underlying per-replicate count matrix or synthetic barcode identifiers.
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 · 8 definitions
- amplicon
- Population STARR-seq amplicon identifier
- haplotype
- Haplotype identifier within the amplicon
- effect_ratio
- Official haplotype regulatory effect ratio from GSE77743
- log2_effect
- Signed log2 transformation of effect_ratio
- abs_log2_effect
- Absolute log2 effect supplied by the GEO release or derived when absent
- padj
- Adjusted p-value supplied by the GEO release
- significant_fdr_05
- Convenience flag indicating padj less than 0.05
- qc_pass
- True for records retained after structural and finite-value QC
Quality control
Retained records only when amplicon and haplotype identifiers, a positive finite effect ratio, and a finite adjusted p-value were present. All 1,153 released records passed this structural QC. significant_fdr_05 is reported separately and was not used to remove neutral or nonsignificant haplotypes. The BIRD supplement separately reports 173 high-coverage HepG2 variants, but the public effect release does not expose the raw counts needed to reproduce that subset.
Curation notes
This is the public Guo et al. 2017 Pop-STARR-seq HepG2 dataset used as the HepG2 fetal-adiposity-locus benchmark by Majoros et al.; it is not the target paper's new adipocyte or pre-adipocyte run. The GEO series title mentions preadipocytes pre/post differentiation, but the sample metadata and overall design identify HepG2. The official haplotype FASTA is retained in raw_data for sequence lookup.