FAIRE-STARR-seq enhancer activity in U2OS-AR and U2OS-GR after cognate hormone treatment
Androgen and glucocorticoid receptor direct distinct transcriptional programs by receptor-specific and shared DNA binding sitesA FAIRE-derived genomic fragment library was cloned into an episomal human STARR-seq vector and transfected into stable receptor-expressing U2OS-AR and U2OS-GR cells. Each cell line was assayed with vehicle and cognate hormone treatment in three biological replicates, and reporter transcripts were sequenced with 8-nt UMIs.
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
U2OS-AR: 5 nM R1881 or DMSO vehicle for 14 h; U2OS-GR: 1 µM dexamethasone or ethanol vehicle for 14 h
FAIRE-STARR-seq variant using accessible genomic fragments isolated from dexamethasone-treated U2OS-GR cells to build the common library. Inserts were cloned into the human STARR-seq vector (Addgene #71509) and transcribed enhancer fragments were quantified by paired-end RNA sequencing after an 8-nt UMI was introduced during reverse transcription. The deposited assay contains U2OS-AR DMSO/R1881 and U2OS-GR ethanol/dexamethasone conditions, three biological replicates per condition, with author-merged RPKM-normalized BigWig tracks.
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 · 12 definitions
- element_id
- Stable identifier for the derived 1-kb hg19 genomic bin; this is not an original oligo or barcode identifier.
- chrom
- Canonical hg19 chromosome name.
- start
- 0-based inclusive start coordinate of the derived 1-kb bin.
- end
- 0-based exclusive end coordinate of the derived hg19 genomic bin; bins are 1 kb except for a terminal bin truncated at the chromosome end.
- ar_dmso_mean_rpkm
- Mean author-provided RPKM signal across the bin for U2OS-AR vehicle (DMSO), merged three-replicate track.
- ar_r1881_mean_rpkm
- Mean author-provided RPKM signal across the bin for U2OS-AR plus 5 nM R1881, merged three-replicate track.
- gr_etoh_mean_rpkm
- Mean author-provided RPKM signal across the bin for U2OS-GR vehicle (ethanol), merged three-replicate track.
- gr_dex_mean_rpkm
- Mean author-provided RPKM signal across the bin for U2OS-GR plus 1 µM dexamethasone, merged three-replicate track.
- ar_r1881_vs_dmso_log2
- Log2 hormone-versus-vehicle signal ratio for AR, calculated as log2((ar_r1881_mean_rpkm + 0.1)/(ar_dmso_mean_rpkm + 0.1)).
- gr_dex_vs_etoh_log2
- Log2 hormone-versus-vehicle signal ratio for GR, calculated as log2((gr_dex_mean_rpkm + 0.1)/(gr_etoh_mean_rpkm + 0.1)).
- max_mean_rpkm
- Maximum of the four condition-specific mean RPKM values for the bin.
- n_conditions_detected
- Number of the four condition-specific tracks with positive signal in the bin.
Quality control
The authors mapped reads to hg19 with Bowtie2 v2.1.0 (--very-sensitive), deduplicated reads by UMI and genomic coordinates with UMI-tools v1.0.0, filtered reads with SAMtools MAPQ <10, merged biological-replicate BAM files, and generated RPKM-normalized BigWig tracks with deepTools bamCoverage. For the derived table, only finite 1-kb bins with positive signal in at least one source track were retained; bins on non-canonical hg19 contigs (chrM, chrUn, and random/unlocalized contigs) were additionally excluded to keep the table on canonical hg19 chromosomes, consistent with the article's peak analysis.
Curation notes
ArrayExpress E-MTAB-9614 provides four author-merged RPKM BigWig tracks and IDF/SDRF metadata, but no per-oligo barcode-count matrix. table.csv is therefore a derived, non-overlapping 1-kb union of the deposited signal tracks: BigWig bedGraph intervals were integrated over each bin, condition tracks were joined by hg19 coordinates, and hormone/vehicle log2 ratios were calculated with a 0.1-RPKM pseudocount. U2OS-AR and U2OS-GR are engineered stable receptor-expressing derivatives of parental U2OS; CVCL:0042 resolves the parental U2OS Cellosaurus entry. The individual AQP3/IP6K3 reporter constructs are targeted validation assays and are represented in the supplemental PDF, but are not mixed into this genome-wide FAIRE-STARR-seq table.