Experiment / E5OYZ0XNTTargeted / Cap-STARR-seq

snpSTARRseq enhancer activity in LNCaP cells - 48 h post-transfection

Optimized high-throughput screening of non-coding variants identified from genome-wide association studies

A capture-enriched human genomic-fragment library containing prostate-cancer-associated SNP loci and positive/negative control regions was transiently transfected into LNCaP prostate cancer cells in three biological replicas. Reporter RNA self-transcription was normalized to plasmid DNA input and reference-versus-alternative allele activity was tested with negative-binomial regression at the 48 h harvest.

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Organism: Human
Taxonomy ID: NCBITaxon:9606
Biosample: CVCL:0395
Reference genome: hg19
Design focus: Variant-focused
Region of interest: Not reported / not applicable

Perturbation & assay details

Basal / Untreated; 48 h post-transfection

snpSTARRseq used pooled human genomic DNA (NA13421; 27 male and 27 female CEPH/Utah donors), 500-800 bp fragmentation, hybridization capture, and cloning into the second-generation hSTARR-ORI plasmid (Addgene #99296). The resulting episomal library used UMI-tagged fragments (mean insert length about 543 bp; reconstructed up to 841 bp) and was transfected at 100 micrograms plasmid per 5 x 10^7 cells. mRNA was poly(A)-selected, reverse-transcribed with a plasmid-specific primer, and amplified at the reporter junction; DNA input and RNA libraries were sequenced by asymmetric paired-end MiSeq/HiSeq protocols. The negative-binomial regression model compared alternative- and reference-supporting RNA counts with plasmid DNA count as an offset, yielding the reported log2 ALT/REF enhancer effect; PacBio CCS was used to validate insert reconstruction.

Processed data

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

Visible columns (25 of 25)

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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 · 25 definitions

variant_id: Generated stable key in the form chromosome:position:reference>alternate.
event: Authors' semicolon-delimited event identifier: chromosome;1-based hg19 position;reference allele;alternate allele.
rsid: dbSNP rs identifier; blank for the 12 Coriell-specific events without a reported rsID.
chromosome: Chromosome reported for the event on hg19.
position_hg19: 1-based event coordinate on hg19.
reference_allele: Reference allele supported by the reconstructed enhancer fragments.
alternate_allele: Alternative allele supported by the reconstructed enhancer fragments.
capture_region: Broad capture interval from total500.bed, represented as chromosome:start-end; source coordinates are 0-based half-open BED coordinates.
capture_region_labels: Comma-delimited labels assigned to the capture interval by the authors, including SNP, positive-control, or negative-control labels.
capture_design_class: Derived capture class: SNP-targeted_capture, positive_control, or negative_control.
pca_original_target: Boolean derived from the raw ORIGINAL flag: true for ORIGINAL=original, false for ORIGINAL=NO, blank for source NA.
ref_unique_plasmids: Number of unique reconstructed plasmid fragments supporting the reference allele (raw ref_count).
alt_unique_plasmids: Number of unique reconstructed plasmid fragments supporting the alternate allele (raw alt_count).
ref_mrna_counts: Reference-allele reporter mRNA/self-transcription count (raw ref_expr).
alt_mrna_counts: Alternate-allele reporter mRNA/self-transcription count (raw alt_expr).
reported_alt_frequency: ALT frequency reported by the authors' result pipeline (raw alt_freq; not recomputed).
alt_effect_log2: Negative-binomial regression log2 enhancer activity effect for ALT relative to REF (raw alt_effect).
p_value: Nominal p-value from the authors' negative-binomial reference-versus-alternate test.
fdr: Benjamini-Hochberg adjusted p-value calculated across the 308 QC-passing events in this time point.
nominal_significant_p_lt_0_05: Boolean indicating p_value < 0.05.
fdr_significant_q_lt_0_05: Boolean indicating fdr < 0.05.
z_score: NBR z statistic reported by the authors.
g5_status: Reported G5 annotation flag from the raw result table (G5_TRUE or G5_FALSE when available).
source_original_label: Raw ORIGINAL label from the authors' result table (original or NO when available).
timepoint_hours: Harvest time after transfection, in hours.

Quality control

The authors reconstructed and UMI/sequence-matched full enhancer fragments, then retained SNP/event rows with at least 15 unique REF and 15 unique ALT plasmids; the repository's reproducible code uses ref_count >= 15 and alt_count >= 15. Package QC retained 308 of 456 raw NBR rows for this time point, and the retained event set matches the authors' 308.bed. P-values are the authors' negative-binomial regression results; FDR is Benjamini-Hochberg adjustment across the 308 retained rows. All retained rows have finite event coordinates and counts and are kept regardless of nominal significance.

Curation notes

This is the 48 h harvest of the shared snpSTARRseq library and the principal time point used for several manuscript comparisons. The processed table has 308 rows (63 p < 0.05; 16 BH FDR < 0.05), including 102 original PCa target events, 234 SNP-targeted capture events, 29 positive-control events, 45 negative-control events, and 12 events without an rsID. LNCaP was resolved to Cellosaurus CVCL:0395.

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