Companion DiR-seq allele-specific MPRA in LNCaP cells
Parallel Reporter Assays Identify Altered Regulatory Role of rs684232 in Leading to Prostate Cancer PredispositionThe GEO series linked to this publication contains a companion episomal DiR-seq MPRA run in human LNCaP prostate cancer cells using the same 55-bp allele-specific risk-SNP library. Three RNA/cDNA reporter libraries were compared with two LNCaP-specific plasmid-input libraries.
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
The DiR-seq construct was a pGL3-derived episomal reporter with a 450-bp dinucleotide-barcoded reporter region downstream of a 55-bp SNP-centered allele insert placed immediately upstream of the basal SV40 promoter. Illumina HiSeq X-TEN 150-bp paired-end reads quantified RNA/cDNA barcodes and LNCaP plasmid-input DNA barcodes.
Processed data
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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 · 36 definitions
- variant_id
- dbSNP rs identifier for the tested variant.
- gwas_catalog_chromosome
- Chromosome field copied from the publication's GWAS Catalog Table S1; the table does not separately state its coordinate build.
- gwas_catalog_position
- Position field copied from the publication's GWAS Catalog Table S1; the table does not separately state its coordinate build.
- reported_genes
- Gene or genes reported for the GWAS association in Table S1.
- mapped_gene
- Gene mapping reported in Table S1.
- sequence_context
- Variant context annotation reported in Table S1.
- allele_1
- First tested allele, sorted alphabetically; the library contains one mapped barcode per listed allele.
- allele_2
- Second tested allele, sorted alphabetically.
- allele_3
- Third tested allele for the three mapped multi-allelic SNP IDs; blank for biallelic variants.
- allele_1_barcode
- GEO barcode identifier mapped to allele_1.
- allele_2_barcode
- GEO barcode identifier mapped to allele_2.
- allele_3_barcode
- GEO barcode identifier mapped to allele_3; blank for biallelic variants.
- allele_1_mean_dna_cpm
- Mean LNCaP plasmid-input DNA barcode counts per million across two input replicates for allele_1.
- allele_2_mean_dna_cpm
- Mean LNCaP plasmid-input DNA barcode counts per million across two input replicates for allele_2.
- allele_3_mean_dna_cpm
- Mean LNCaP plasmid-input DNA barcode counts per million across two input replicates for allele_3; blank for biallelic variants.
- allele_1_mean_rna_cpm
- Mean LNCaP RNA/cDNA reporter barcode counts per million across three RNA replicates for allele_1.
- allele_2_mean_rna_cpm
- Mean LNCaP RNA/cDNA reporter barcode counts per million across three RNA replicates for allele_2.
- allele_3_mean_rna_cpm
- Mean LNCaP RNA/cDNA reporter barcode counts per million across three RNA replicates for allele_3; blank for biallelic variants.
- allele_1_log2_activity
- Mean replicate log2 RNA/DNA reporter activity for allele_1, using a 0.5-CPM pseudocount.
- allele_2_log2_activity
- Mean replicate log2 RNA/DNA reporter activity for allele_2, using a 0.5-CPM pseudocount.
- allele_3_log2_activity
- Mean replicate log2 RNA/DNA reporter activity for allele_3; blank for biallelic variants.
- allele_2_vs_allele_1_log2_fc
- Allele_2 minus allele_1 mean log2 reporter activity; positive values indicate higher activity for allele_2.
- allele_2_vs_allele_1_p_value
- Paired two-tailed t-test p-value for the allele_2 versus allele_1 activity difference across three RNA replicates.
- allele_3_vs_allele_1_log2_fc
- Allele_3 minus allele_1 mean log2 reporter activity; blank for biallelic variants.
- allele_3_vs_allele_1_p_value
- Paired two-tailed t-test p-value for allele_3 versus allele_1 across three RNA replicates; blank for biallelic variants.
- allele_3_vs_allele_2_log2_fc
- Allele_3 minus allele_2 mean log2 reporter activity; blank for biallelic variants.
- allele_3_vs_allele_2_p_value
- Paired two-tailed t-test p-value for allele_3 versus allele_2 across three RNA replicates; blank for biallelic variants.
- risk_allele
- Strongest SNP-risk allele from Table S1 when available.
- protective_allele
- The other allele for a biallelic variant with a resolved Table S1 risk allele; blank when the mapping is multi-allelic or unresolved.
- risk_vs_protective_ratio
- Reporter activity ratio for risk allele divided by protective allele, when resolvable.
- risk_vs_protective_log2_fc
- Risk-allele minus protective-allele mean log2 reporter activity; negative values indicate lower risk-allele activity.
- risk_vs_protective_p_value
- Paired two-tailed t-test p-value for the risk-versus-protective activity difference across three RNA replicates.
- gwas_risk_allele_frequency
- Risk-allele frequency reported in Table S1.
- gwas_association_p_value
- GWAS association p-value reported in Table S1.
- paper_reported_regulatory_hit
- Blank because the publication's cell-specific Supplementary Table S6 lists 22Rv1 hits only; no LNCaP hit list was provided.
- min_raw_count
- Minimum raw barcode count across all listed allele barcodes, three RNA replicates, and two LNCaP DNA-input replicates.
Quality control
The authors used FastP (retaining the 5-prime terminal N base), Pandaseq paired-read assembly, ShortRead sub-library sorting/counting, library-size normalization to 1 million reads, Pearson replicate-consistency checks, and two-tailed Student's t-tests for allelic expression. For this package, a mapped SNP was retained only when every allele barcode had at least 10 raw counts in each of the three RNA/cDNA files and both LNCaP plasmid-input files; this retained 208 of 211 mapped SNP IDs and excluded rs1456315, rs76934034, and rs7789197. Processed activities are mean replicate log2((RNA CPM + 0.5)/(DNA CPM + 0.5)); reported p-values are paired two-tailed t-tests across the three RNA replicates.
Curation notes
The final article narrative and Supplementary Table S6 focus on 22Rv1, but the same linked GEO series contains LNCaP DiR-seq RNA and LNCaP-specific input libraries. This table captures that companion deposited MPRA run and does not treat the later single-variant luciferase assays as MPRA data. The barcode mapping contains 211 SNP IDs and 425 allele constructs, including three mapped multi-allelic IDs; five mapped IDs have no matching Table S1 annotation. Pairwise Pearson correlations across the three LNCaP RNA barcode-count profiles were 0.7691, 0.9027, and 0.9474. The first pair is lower than the other replicate correlations, but the run was retained because count-level QC passed for the included variants; numeric activity and p-value columns were regenerated from the deposited GEO counts. No LNCaP-specific hit list was available in the paper, so the paper hit flag is blank.