Experiment / E2IMJLMJLTargeted / Cap-STARR-seq

Additional randomized ARBS capture-STARR-seq validation library

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

The flagged paper randomly sampled 2,495 ARBS across its ranked universe for an additional capture-STARR-seq library in LNCaP cells. The deposited public data contain two vehicle RNA replicates and one DNA input track; the table reports their interval summaries alongside the paper's active/inactive labels.

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

Deposited RNA tracks: EtOH vehicle after DMSO pretreatment; paper reports a parallel 10 nM DHT arm, but no DHT RNA track is deposited in GSE217319

Capture-STARR-seq constructs were designed by unbiased random sampling across the 69,330 ranked ARBS universe. The paper downsampled and merged two vehicle RNA replicates, then used k-means signal clusters to call 149 active and 2,346 inactive sites. GSE217319 provides two vehicle mRNA BigWigs and one capture-library DNA input BigWig; the processed ratios are derived from mean0 interval signals with a 0.01 pseudocount and should not be interpreted as the paper's original count-based differential statistic.

Processed data

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

Visible columns (16 of 16)

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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 · 16 definitions

element_id: Enhancer ID (enhid) in this paper's ranked ARBS universe.
chrom: Chromosome in hg19.
start: Start coordinate from the paper's 1B_tumor source-data table.
end: End coordinate from the paper's 1B_tumor source-data table.
element_length: ARBS interval length in base pairs.
patient_prevalence: Number of primary tumors containing the ARBS.
prevalence_bin: Paper-defined ARBS prevalence bin: SH, PS, or UN.
paper_activity_class: Paper source-data class for the additional library: active or inactive.
vehicle_rna_rep1_mean_signal: Mean vehicle STARR-seq RNA signal across the ARBS interval for GSE217319 replicate 1.
vehicle_rna_rep2_mean_signal: Mean vehicle STARR-seq RNA signal across the ARBS interval for GSE217319 replicate 2.
vehicle_rna_mean_signal: Arithmetic mean of the two deposited vehicle RNA replicate interval means.
dna_input_mean_signal: Mean signal across the ARBS interval in the deposited capture-library DNA input track.
vehicle_rep1_over_dna_log2: Derived log2((vehicle RNA replicate 1 + 0.01)/(DNA input + 0.01)).
vehicle_rep2_over_dna_log2: Derived log2((vehicle RNA replicate 2 + 0.01)/(DNA input + 0.01)).
vehicle_rna_over_dna_log2: Derived log2((vehicle RNA mean + 0.01)/(DNA input + 0.01)); 0.01 is the documented signal pseudocount.
vehicle_rna_replicate_cv: Population coefficient of variation across the two vehicle RNA replicate interval means; blank when the mean is zero.

Quality control

The paper's active/inactive calls were based on k-means clustering of downsampled vehicle STARR-seq signal (149 active; 2,346 inactive). For this package, all 2495/2495 sites had valid hg19 intervals and finite values in both RNA replicates and the DNA input track and were retained; no intensity cutoff was applied because the inactive class is a reported biological result. Retained 2495 rows; excluded 0.

Curation notes

GSE217319 sample metadata describe the deposited RNA samples as EtOH and DMSO treatment and the DNA sample as no treatment. The article methods state that the additional library was also treated with 10 nM DHT, but a DHT RNA signal track is not present in the public series files; therefore this table does not invent a DHT measurement.

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