BAC/fosmid targeted PCOS GWAS STARR-seq in COV434 cells
Gene regulatory activity associated with polycystic ovary syndrome revealed DENND1A-dependent testosterone productionA targeted episomal STARR-seq library was constructed from approximately 400 bp fragments of BACs and fosmids spanning 14 PCOS GWAS loci and transfected into human COV434 ovarian cells. The processed table contains the 464 CRADLE/DESeq2 regulatory-element calls reported at Benjamini-Hochberg FDR <= 0.5%.
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 STARR-seq using the STARR-seq ORI vector (Addgene #99296). Genomic fragments sheared from the selected BAC/fosmid library were cloned into the vector, and the plasmid pool was transfected into COV434 cells (50 million cells and 100 micrograms per biological replicate; three biological replicates); reporter RNA was collected 6 hours after transfection. Three assay-library and three reporter-library RPKM bigWig tracks are packaged in raw_data. Regulatory activity was measured as a CRADLE-corrected DESeq2 pseudo-log2 fold change.
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 · 13 definitions
- element_id
- Stable identifier derived from cell line and the unique GRCh38 genomic interval.
- chromosome
- GRCh38 chromosome name from the supplementary STARR-seq call.
- start
- Zero-based inclusive genomic start coordinate from Supplementary Data 4.
- end
- Zero-based exclusive genomic end coordinate from Supplementary Data 4.
- length_bp
- Element interval length in base pairs, calculated as end minus start.
- locus
- PCOS GWAS locus label from the final BAC/fosmid interval in Supplementary Data 2 that overlaps the element.
- source_bac_fosmid_ids
- Semicolon-separated BAC or fosmid identifiers from Supplementary Data 2 whose final-library intervals overlap the element.
- activity_direction
- Increasing when the reported pseudo-log2 fold change is positive and decreasing when it is negative; increasing and decreasing activity correspond to enhancer-like and repressor-like activity in the paper's interpretation.
- pseudo_log2_fold_change
- CRADLE-corrected DESeq2 pseudo-log2 fold-change effect size reported in Supplementary Data 4.
- bh_adjusted_p_value
- Two-sided Benjamini-Hochberg adjusted p-value reported with the STARR-seq regulatory-element call.
- overlaps_cell_line_atac
- TRUE when the element overlaps a COV434 ATAC-seq region listed in Supplementary Data 6; otherwise FALSE.
- source_supplementary_data
- Supplementary workbook sheet from which the activity result was taken.
- qc_status
- Package retention status; PASS_PAPER_FDR_0.005 indicates the paper-defined FDR threshold and package-level interval checks passed.
Quality control
The study assessed sequencing quality with FastQC, trimmed adapters with Trimmomatic, aligned input and reporter libraries to hg38 with Bowtie2, retained properly paired reads with MAPQ >= 30 outside centromeres and blacklist regions, marked duplicates with Picard, and generated RPKM signal tracks. CRADLE was used for bias correction and peak calling and DESeq2 for effect-size estimation; candidate calls were retained at Benjamini-Hochberg FDR <= 0.005. Package QC required finite effect and adjusted-p values, positive-length valid genomic intervals, unique coordinates, and overlap with a final BAC/fosmid interval; all 464 source rows passed.
Curation notes
This is a targeted, region-focused STARR-seq screen rather than a direct allele-contrast library. The 464 rows are the paper's COV434 regulatory-element calls, not the 486 PCOS association variants tested later. BAC/fosmid locus labels were joined by genomic interval, and COV434 ATAC overlap was joined from Supplementary Data 6. The packaged GEO tracks are RPKM-normalized input/output signal tracks; the source workbook provides the paper's final effect sizes and adjusted p-values. COV434 is represented by Cellosaurus CVCL:2010; the current Cellosaurus record notes that this line has been reclassified, although the paper used it as an ovarian granulosa model.