DENND1A-locus allele-specific targeted STARR-seq in H295R cells
Gene regulatory activity associated with polycystic ovary syndrome revealed DENND1A-dependent testosterone productionGenomic DNA from five healthy female 1000 Genomes individuals was enriched across the DENND1A locus, cloned into an episomal STARR-seq vector, pooled, and assayed in H295R cells. The processed table retains the 62 of 623 assayed variants with BIRD posterior probability greater than 0.90 for an allele-specific regulatory effect.
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
A targeted, episomal STARR-seq adaptation. Genomes from three European-ancestry and two Han Chinese-ancestry healthy female 1000 Genomes individuals were sheared to approximately 200 bp, captured with Agilent SureSelect custom probes spanning GRCh38 chr9:123279654-124030107, cloned into the STARR-seq ORI vector, pooled equimolarly, and transfected into H295R cells (70 million cells and 140 micrograms per replicate; three biological replicates). Input and reporter libraries were sequenced, allele counts were obtained after WASP/Bowtie2 processing and samtools mpileup, and BIRD estimated theta as the alternate-allele transcriptional rate relative to the reference allele.
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 · 20 definitions
- variant_id
- dbSNP rsID of the tested variant from Supplementary Data 11.
- chromosome
- GRCh38 chromosome for the tested variant, when supplied by Supplementary Data 11 or the matching Data 12 annotation.
- position_hg38
- 1-based GRCh38 variant position; blank when the source did not supply a coordinate.
- ref_allele
- Reference allele reported in the source BIRD input/output summary.
- alt_allele
- Alternate allele reported in the source BIRD input/output summary.
- alt_allele_frequency
- Alternate-allele frequency (af) in the pooled 1000 Genomes source population.
- minor_allele
- Whether the minor allele is the reference allele (REF) or alternate allele (ALT), as reported by the source.
- minor_allele_frequency
- Minor-allele frequency (MAF) reported in Supplementary Data 11.
- theta_alt_over_ref
- BIRD posterior-median effect size theta, interpreted as alternate-allele transcriptional rate divided by reference-allele transcriptional rate.
- theta_lower_95ci
- Lower bound of the BIRD 95% credible interval for theta.
- theta_upper_95ci
- Upper bound of the BIRD 95% credible interval for theta.
- posterior_probability
- BIRD posterior probability P of a regulatory effect; rows were retained at P > 0.90.
- standard_error
- BIRD standard error for theta reported in Supplementary Data 11.
- alternate_allele_activity
- Derived direction relative to the alternate allele: increased for theta > 1, decreased for theta < 1, and unchanged for theta = 1.
- minor_allele_activity
- Derived direction for the minor allele, reversing the alternate-allele direction when the minor allele is REF.
- orthogonal_overlap
- ENCODE ATAC/DNase or enhancer-like element annotation joined from Supplementary Data 12, when available.
- eqtl_gene
- GTEx eQTL gene annotation joined from Supplementary Data 12, when available.
- coordinate_source
- Supplementary Data 11 when the source supplied coordinates; Supplementary Data 12 when its matching position filled missing Data 11 coordinates.
- supplementary_annotation_status
- Whether a matching rsID was present in Supplementary Data 12; Data 12-only variants were not added to the BIRD result set.
- qc_status
- Package retention status; PASS_PAPER_BIRD_P_GT_0.90 indicates the paper-defined posterior-probability filter and value/ID checks passed.
Quality control
The paper retained reads with MAPQ >= 30 outside centromeres and blacklist regions, used WASP and Bowtie2 for allele-aware alignment, marked duplicates with Picard, and assigned variant allele counts with samtools mpileup. BIRD was run with its standard model and a regulatory-effect threshold of 1.2; the source table contains 623 assayed variants. Package QC retained the paper-defined 62 variants with posterior probability P > 0.90, finite theta/credible interval/standard-error values, and unique variant IDs. Three retained variants lack genomic coordinates and allele fields in Supplementary Data 11; those missing source values remain blank rather than being imputed, except that the matching Supplementary Data 12 position was used for rs894139170.
Curation notes
This is the study's genuine allele-specific MPRA/STARR-seq experiment. The 62 retained rows are the paper's BIRD-positive variants from Supplementary Data 11, not the nearby PCOS GWAS association summary statistics. The raw_data folder includes the three input and three reporter RPKM tracks, the complete source workbook, and the five 1000 Genomes sample IDs. The alternate_allele_activity and minor_allele_activity fields are deterministic interpretations of BIRD theta; no new statistical effect estimates were recomputed from the RPKM tracks. Supplementary Data 11 and Data 12 are not perfectly identical: 59 high-probability rsIDs join directly, three Data 11 candidates have no Data 12 annotation, and three Data 12 annotations are not in the retained Data 11 P > 0.90 set.