Experiment / E7UGOX7XTTargeted / Cap-STARR-seq

LNCaP ARBS capture-STARR-seq: DHT versus EtOH vehicle

Extensive androgen receptor enhancer heterogeneity in primary prostate cancers underlies transcriptional diversity and metastatic potential

Published 3-replicate capture-STARR-seq assay of androgen receptor binding-site fragments in LNCaP cells, with 10 nM DHT or EtOH vehicle for 4 h. The table summarizes all 3,230 GSE151064 ARBS intervals and adds their overlap with the flagged paper's ranked ARBS universe.

Download processed table (CSV)Raw source data API documentation

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:0395
Reference genome: hg19
Design focus: Region-focused
Region of interest: Not reported / not applicable

Perturbation & assay details

10 nM DHT for 4 h versus 100% EtOH vehicle control

Capture-based episomal STARR-seq using sheared pooled male genomic DNA hybridized to probes across approximately 700-bp clinical ARBS, cloned downstream of a minimal promoter. Public GSE151064 BigWigs are normalized interval signal tracks; the table reports mean0 interval signal and derived DHT/EtOH and RNA/input ratios rather than re-running the original DESeq2 count model. DHT and EtOH each have three biological RNA replicates, with a no-treatment library/input track.

Processed data

50 rows per page. Click a cell to inspect its full value.

Visible columns (24 of 24)

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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 · 24 definitions

element_id: Unique identifier from the GSE151064 ARBS capture interval.
chrom: Chromosome in hg19.
start: 0-based start coordinate of the 700-bp capture interval.
end: 0-based, half-open end coordinate of the capture interval.
element_length: Capture interval length in base pairs.
source_activity_class: Original GSE151064 STARR-seq class: inducible, constitutive, or inactive.
current_enhid: Semicolon-separated enhancer ID(s) from this paper's 69,330-region ranked ARBS universe that overlap the capture interval; blank means no overlap.
current_patients: Number of primary tumors containing each overlapping current-paper ARBS.
current_prevalence_bin: Current-paper prevalence bin for overlapping ARBS (SH, PS, or UN).
current_activity_class: Current-paper source-data functional label for overlapping ARBS.
dht_rep1_mean_rpkm: Mean normalized DHT STARR-seq signal across the capture interval for biological replicate 1, from GSE151064 BigWig.
dht_rep2_mean_rpkm: Mean normalized DHT STARR-seq signal across the capture interval for biological replicate 2, from GSE151064 BigWig.
dht_rep3_mean_rpkm: Mean normalized DHT STARR-seq signal across the capture interval for biological replicate 3, from GSE151064 BigWig.
etoh_rep1_mean_rpkm: Mean normalized EtOH vehicle STARR-seq signal across the capture interval for biological replicate 1, from GSE151064 BigWig.
etoh_rep2_mean_rpkm: Mean normalized EtOH vehicle STARR-seq signal across the capture interval for biological replicate 2, from GSE151064 BigWig.
etoh_rep3_mean_rpkm: Mean normalized EtOH vehicle STARR-seq signal across the capture interval for biological replicate 3, from GSE151064 BigWig.
dht_mean_rpkm: Arithmetic mean of the three DHT replicate interval means.
etoh_mean_rpkm: Arithmetic mean of the three EtOH replicate interval means.
library_input_mean_rpkm: Mean normalized signal across the interval in the no-treatment STARR-seq library/input track.
dht_vs_etoh_log2fc: Derived log2((DHT mean + 0.01)/(EtOH mean + 0.01)); 0.01 is the documented signal pseudocount.
dht_over_input_log2: Derived log2((DHT mean + 0.01)/(library input + 0.01)).
etoh_over_input_log2: Derived log2((EtOH mean + 0.01)/(library input + 0.01)).
dht_replicate_cv: Population coefficient of variation across DHT replicate interval means; blank when the mean is zero.
etoh_replicate_cv: Population coefficient of variation across EtOH replicate interval means; blank when the mean is zero.

Quality control

GSE151064 processing removed indel-containing and low-MAPQ (less than 60) reads, excluded ENCODE blacklist regions, and applied the source study's DESeq2 activity classification. All 3230/3230 source intervals had valid coordinates and finite summaries in all seven public tracks and were retained; no signal cutoff was added because low signal defines the biologically meaningful inactive class. Retained 3230 rows; excluded 0.

Curation notes

This is a quantitative reporter dataset generated in the cited Huang et al. (2021) study and reused by the flagged paper. GSE151064 contains 286 inducible, 465 constitutive, and 2,479 inactive capture intervals. The flagged paper's overlap table labels 286, 463, and 2,467 overlapping ARBS respectively; 15 GSE intervals do not overlap the 69,330-region ranked universe and one capture interval overlaps two ranked ARBS, so the table preserves the original GSE interval granularity and provides a semicolon-separated crosswalk.

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