Pooled whole-genome STARR-seq in LNCaP cells
Functional assessment of human enhancer activities using whole-genome STARR-sequencingAn episomal WHG-STARR-seq library of randomly sheared human genomic fragments was tested in the human prostate cancer cell line LNCaP using the SCP1 minimal promoter. Two biological replicates were pooled for MACS2 peak calling against the input plasmid library; the packaged table contains 94,527 unique active enhancer peaks passing the reported q-value 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.
Perturbation & assay details
Basal / Untreated
Episomal self-transcribing reporter assay using 350–650 bp size-selected fragments from random human genomic DNA, with an average fragment length of approximately 500 bp. Inserts were cloned downstream of the SCP1 minimal promoter and into the reporter 3' UTR; the input plasmid library served as the DNA baseline and the poly(A)-selected self-transcribed RNA output was the activity readout. Paired-end 2 × 100 bp sequencing was aligned to hg19, and the authors used uniquely mapped distinct fragments, pooled across 16 indexing libraries per replicate, for combined two-replicate MACS2 peak calling.
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 · 16 definitions
- element_id
- Unique WHG-STARR-seq peak identifier from the GEO processed file.
- chromosome
- Human hg19 chromosome name.
- start_hg19_0based
- BED interval start coordinate on hg19, zero-based and inclusive.
- end_hg19_0based_exclusive
- BED interval end coordinate on hg19, zero-based and exclusive.
- length_bp
- Peak interval length in base pairs, calculated as end minus start.
- macs2_score
- Integer score from the deposited MACS2 narrowPeak-style record.
- enhancer_activity_fold_enrichment
- MACS2 signal/enrichment value; the paper uses this enrichment score as WHG-STARR-seq enhancer activity.
- p_value_neg_log10
- MACS2 peak significance reported as -log10(p-value).
- q_value_neg_log10
- MACS2 multiple-testing significance reported as -log10(q-value).
- p_value
- P-value derived from the deposited -log10(p-value) field as 10 raised to the negative reported value.
- q_value
- Q-value derived from the deposited -log10(q-value) field as 10 raised to the negative reported value.
- summit_offset_bp
- MACS2 summit offset from the peak interval start in base pairs.
- chromatin_context
- Active enhancer context classified by overlap with the LNCaP DNase I sites: open for an overlap and closed for no overlap.
- dnase_peak_count
- Number of unique deposited DNase I peaks overlapping the WHG-STARR-seq peak; zero for closed peaks.
- dnase_peak_ids
- Semicolon-separated identifiers of overlapping deposited DNase I peaks; empty for closed peaks.
- source_file
- GEO processed source file used for the row, indicating the open/closed enhancer partition.
Quality control
The authors filtered multi-mapping reads, collapsed fragments with identical inferred start and end positions using Picard, pooled distinct fragments from the 16 indexing libraries for each replicate, combined the two biological replicates, and called active peaks with MACS2 at q-value < 0.05 using the input plasmid library as background. For this package, records were additionally required to have valid genomic intervals, complete numeric peak fields, and q-value <= 0.05; repeated STARR–DNase overlap rows were collapsed to one row per unique STARR peak. No records were removed by these package-level checks.
Curation notes
This is a region-focused, non-allelic assay: the library was made from random sheared genomic DNA and does not provide rsIDs or reference/alternative allele contrasts. GEO's enhancer_overlap_dnase file contains one row per overlap, so its 12,971 rows were aggregated to 11,980 unique open STARR peaks; the 82,547 non-overlap rows were already unique. The final table therefore has 94,527 rows, matching the paper's reported active enhancer count, with 11,980 open and 82,547 closed peaks. The two biological STARR-seq replicates are represented as one pooled experiment because the authors pooled them for final peak calling. The accompanying ATAC-seq and RNA-seq files are retained in raw_data as study context and provenance, not merged into the MPRA activity table.