Whole-genome STARR-seq in A549, vehicle control (0 h)
Human genome-wide measurement of drug-responsive regulatory activityThe GM12878-derived whole-genome STARR-seq plasmid library was transfected into A549 cells and assayed after the vehicle-control 0 h condition across five biological replicate plates. The table contains the public union of MACS2-called baseline active regions; differential drug-response statistics are not defined for this control.
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
Vehicle control (equal-volume ethanol), 0 h dex exposure
An episomal whole-genome STARR-seq library was built by shearing GM12878 genomic DNA to approximately 350–450 bp and cloning fragments into the 3′ UTR of a reporter plasmid. A549 cells were transfected on 500 cm² plates; five plates were harvested per time point after vehicle or 100 nM dexamethasone exposure. Twelve plasmid-input DNA libraries and 25 output RNA libraries were sequenced on Illumina HiSeq 4000. Bowtie2 aligned paired reads to hg38; MACS2 with NCIS scaling called active regions, and edgeR modeled differential activity relative to 0 h.
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 · 18 definitions
- region_id
- Unique package identifier for the baseline active region.
- coordinate
- hg38 interval string copied from the GEO BED source in chr:start-end form.
- chromosome
- Chromosome label parsed from coordinate.
- start
- BED interval start coordinate from the GEO source.
- end
- BED interval end coordinate from the GEO source.
- width_bp
- Interval width calculated as end minus start.
- region_class
- Baseline activity class; all retained rows are active_region.
- timepoint_hours
- Vehicle/dexamethasone exposure duration in hours; 0 for this control.
- treatment
- Condition label for the assayed output library.
- replicate_count
- Number of biological output replicate plates represented by the time point.
- log2_fold_change_vs_0h
- Published differential activity logFC; blank because this is the 0 h reference condition.
- log_cpm
- Published edgeR logCPM differential-analysis field; blank for the baseline activity table.
- F_statistic
- Published edgeR quasi-likelihood F statistic; blank for the baseline activity table.
- p_value
- Published differential-activity p-value; blank for the baseline activity table.
- fdr
- Published Benjamini–Hochberg FDR; blank for the baseline activity table.
- logFC_baseline
- Source Supplementary Data 1 baseline logFC field; not supplied for the GEO peak-only table.
- qc_status
- Package QC status; PASS_MACS2_q0.10_union identifies rows from the public baseline union peak set.
- source
- Original GEO supplementary file used for the row.
Quality control
The authors retained properly paired Bowtie2 alignments with MAPQ ≥30 outside hg38 centromeres, gaps, and blacklist regions; called regions with MACS2 at q ≤0.10 using NCIS-derived scaling; merged overlapping calls into union sets; and reported strong replicate concordance (R >0.91). Package QC retained 9,695 unique valid intervals from the public GSE114063 0 h union BED file, which is already the paper's MACS2 q ≤0.10 union call set. Rows with malformed coordinates or duplicate intervals were excluded.
Curation notes
The library DNA came from GM12878, while the reporter assay was performed in A549; biosample_id therefore resolves the assayed cell line to A-549 (Cellosaurus CVCL:0023). The article Methods reports 0.02% v/v ethanol vehicle, whereas GEO sample metadata reports 0.1% volume; this package uses a generic vehicle label. The supplementary workbook contains only significant DRE rows, not the full 27,498-region count matrix, so the 0 h table uses the compact GEO active-region union. The approximately 26 GB raw GEO archive and very large per-replicate bigWig tracks were omitted; compact peak sets, GEO metadata, and published DRE results are retained.