Genome-scale GR ChIP-enriched STARR-seq reporter assay
Direct GR Binding Sites Potentiate Clusters of TF Binding across the Human GenomeA549 cells were transfected with an episomal STARR-seq library made from GR ChIP-seq fragments and treated with 100 nM dexamethasone or 0.02% ethanol vehicle for 3 h. The table contains the site-level DESeq2 reporter-RNA contrast for the 10,963 GR binding-site subpeaks that passed the publication's statistical-power filter.
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
100 nM dexamethasone for 3 h vs 0.02% ethanol vehicle control
GR ChIP-seq libraries were adapted and cloned into the 3' UTR of the GFP STARR-seq reporter backbone, transfected into A549 cells, and quantified from reporter RNA in three DEX and three ethanol biological replicate libraries. The published site-level statistics are DESeq2 normalized-count results for the DEX-versus-ethanol comparison.
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 · 17 definitions
- element_id
- Published GR subpeak location identifier
- location
- Original Table S2 location string in the form chromosome_start_end
- chromosome
- Human chromosome from Location
- start
- Start of the one-base published subpeak-center interval
- end
- End of the one-base published subpeak-center interval
- peak_center
- Published subpeak-center coordinate, equal to start
- chip_peak_start
- Start of the corresponding 500-bp GR ChIP-seq peak from Table S1
- chip_peak_end
- End of the corresponding 500-bp GR ChIP-seq peak from Table S1
- chip_merged_reads_per_peak
- Merged GR ChIP-seq reads for the corresponding Table S1 peak
- base_mean
- DESeq2 mean normalized count across the reporter libraries
- log2_fold_change_dex_vs_etoh
- DESeq2 log2 fold change in reporter signal for DEX relative to ethanol
- lfc_se
- Standard error of the DESeq2 log2 fold-change estimate
- wald_stat
- DESeq2 Wald test statistic
- pvalue
- DESeq2 p-value for the DEX-versus-ethanol reporter contrast
- padj
- DESeq2 multiple-testing-adjusted p-value
- response_class
- Induced or repressed when padj < 0.05 and log2 fold change has the matching sign; otherwise not_significant
- qc_pass
- True for rows retained after the documented coordinate and numeric-statistic QC
Quality control
The source Table S2 contains 27,432 called GR subpeaks; 10,963 rows with numeric baseMean, log2FoldChange, lfcSE, statistic, p-value, and adjusted p-value were retained, matching the paper's stated sufficient-statistical-power filter. Each retained Location was required to map to a Table S1 500-bp peak centered at Location start; all 10,963 rows passed this coordinate check. No additional effect-size or FDR threshold was applied, so both significant and non-significant assayed sites remain in the table.
Curation notes
This is the primary genome-scale ChIP-reporter experiment, not the endogenous RNA-seq subseries. Location denotes the center of a fixed 500-bp GR ChIP-seq subpeak; it is not a variant identifier. The table intentionally retains the 9,587 source-assayed sites that were powered but not FDR-significant alongside 1,330 induced and 46 repressed sites. A549 resolves to Cellosaurus CVCL:0023.