The GM12878-derived whole-genome STARR-seq plasmid library was transfected into A549 cells and assayed after 100 nM dexamethasone exposure for 1 h across five biological replicate plates. The table contains published induced and repressed dex-responsive elements (DREs) passing the paper's FDR threshold.
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.
Organism
Human
Taxonomy ID
NCBITaxon:9606
Biosample
CVCL:0023
Reference genome
GRCh38
Design focus
Region-focused
Region of interest
Unbiased whole-genome assay (*)
Perturbation & assay details
100 nM dexamethasone for 1 h
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
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Visible columns (18 of 18)
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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 dex-responsive region.
coordinate
hg38 interval string copied from Supplementary Data 1 in chr:start-end form.
chromosome
Chromosome label parsed from coordinate.
start
Interval start coordinate parsed from the reported source interval.
end
Interval end coordinate parsed from the reported source interval.
width_bp
Interval width calculated as end minus start.
region_class
Published response class: induced or repressed.
timepoint_hours
Dexamethasone exposure duration in hours.
treatment
Dexamethasone condition represented by the table.
replicate_count
Number of biological output replicate plates represented by the time point.
log2_fold_change_vs_0h
Published edgeR logFC for reporter activity at this time point relative to 0 h.
log_cpm
Published edgeR logCPM for the differential-analysis region.
F_statistic
Published edgeR quasi-likelihood F statistic.
p_value
Published p-value for differential STARR-seq activity versus 0 h.
fdr
Published Benjamini–Hochberg FDR for differential STARR-seq activity.
logFC_baseline
Published Supplementary Data 1 source field named logFC (baseline), retained verbatim.
qc_status
Package QC status; PASS_paper_FDR_0.05 identifies rows passing the published differential threshold and package validity checks.
source
Original supplementary workbook and sheet 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 tested differential activity with negative-binomial edgeR quasi-likelihood F-tests. Package QC retained 299 unique valid 1 h DRE intervals from Supplementary Data 1 only when the published p-value and FDR were finite, within [0,1], and FDR ≤0.05; duplicate or malformed intervals were excluded. Both induced and repressed rows are retained.
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). Supplementary Data 1 reports significant DREs rather than a complete union-region count matrix, so this table is a compact result table of 1 h DREs (299 rows), not all active regions. 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.