BAC-based STARR-seq validation of GR-bound regions
Direct GR Binding Sites Potentiate Clusters of TF Binding across the Human GenomeSix human BACs containing previously identified DEX-responsive genes were tagmented into an episomal STARR-seq library and assayed in A549 cells after DEX or ethanol treatment. The table is the publication's base-resolution sliding-window DEX-versus-ethanol significance track across the BAC-covered loci.
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
Six BACs (RP11-806F7, RP11-435L21, RP11-139K17, RP11-788A16, CTD-2340K24, and RP11-769H22) were pooled, tagmented, cloned into the human STARR-seq backbone, and transfected into A549 cells. Three DEX and three ethanol reporter-RNA libraries were normalized per the publication, and Wilcoxon signed-rank tests were applied in a sliding 1-bp window across the target BAC regions.
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
- element_id
- One-base identifier constructed as chromosome_start_end
- chromosome
- Human chromosome for the BAC-covered position
- start
- Start coordinate of the one-base sliding-window position
- end
- End coordinate of the one-base sliding-window position
- neglog10_pvalue
- Publication-reported -log10 of the Wilcoxon p-value for the DEX-versus-ethanol BAC STARR-seq contrast
- pvalue
- Wilcoxon p-value reconstructed as 10^(-neglog10_pvalue); values below floating-point range are represented as 0
- significant_p05
- True when the nominal p-value is below 0.05, equivalent to neglog10_pvalue >= -log10(0.05)
- qc_pass
- True for rows retained after chromosome, coordinate, and numeric-value validity QC
Quality control
The source Supplemental Data File 1 was retained only when chromosome matched the six human BAC-covered chromosomes, position was an integer, and the reported -log10(p) value was finite and non-negative. All 1,078,679 numeric source positions passed these validity checks; 127,149 have nominal p < 0.05. The source p-value track does not expose a per-fragment QC flag or adjusted p-value, so no unreported low-count threshold was inferred.
Curation notes
This table is a base-resolution significance track rather than a fragment-level effect-size table: the publication supplied the sliding-window p-values, while the raw_data directory retains the six BAC reporter fragment-count files and seven BAC input-library fragment files for deeper reanalysis. Coordinates are hg19 positions from Supplemental Data File 1; source fragment-count files use BAC clone coordinates. A549 resolves to Cellosaurus CVCL:0023.