DiR-seq allele-specific MPRA in 22Rv1 cells
Parallel Reporter Assays Identify Altered Regulatory Role of rs684232 in Leading to Prostate Cancer PredispositionEpisomal DiR-seq MPRA of 55-bp allele-specific oligos centered on prostate-cancer risk SNPs, transfected into human 22Rv1 prostate cancer cells. Three RNA/cDNA reporter libraries were compared with two 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 plasmid-input DNA barcodes.
Processed data
50 rows per page. Click a cell to inspect its full value.
Visible columns (36 of 36)
| Row | ||||||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | ||||||||||||||||||||||||||||||||||||
| 2 | ||||||||||||||||||||||||||||||||||||
| 3 | ||||||||||||||||||||||||||||||||||||
| 4 | ||||||||||||||||||||||||||||||||||||
| 5 | ||||||||||||||||||||||||||||||||||||
| 6 | ||||||||||||||||||||||||||||||||||||
| 7 | ||||||||||||||||||||||||||||||||||||
| 8 | ||||||||||||||||||||||||||||||||||||
| 9 | ||||||||||||||||||||||||||||||||||||
| 10 | ||||||||||||||||||||||||||||||||||||
| 11 | ||||||||||||||||||||||||||||||||||||
| 12 | ||||||||||||||||||||||||||||||||||||
| 13 | ||||||||||||||||||||||||||||||||||||
| 14 | ||||||||||||||||||||||||||||||||||||
| 15 | ||||||||||||||||||||||||||||||||||||
| 16 | ||||||||||||||||||||||||||||||||||||
| 17 | ||||||||||||||||||||||||||||||||||||
| 18 | ||||||||||||||||||||||||||||||||||||
| 19 | ||||||||||||||||||||||||||||||||||||
| 20 | ||||||||||||||||||||||||||||||||||||
| 21 | ||||||||||||||||||||||||||||||||||||
| 22 | ||||||||||||||||||||||||||||||||||||
| 23 | ||||||||||||||||||||||||||||||||||||
| 24 | ||||||||||||||||||||||||||||||||||||
| 25 | ||||||||||||||||||||||||||||||||||||
| 26 | ||||||||||||||||||||||||||||||||||||
| 27 | ||||||||||||||||||||||||||||||||||||
| 28 | ||||||||||||||||||||||||||||||||||||
| 29 | ||||||||||||||||||||||||||||||||||||
| 30 | ||||||||||||||||||||||||||||||||||||
| 31 | ||||||||||||||||||||||||||||||||||||
| 32 | ||||||||||||||||||||||||||||||||||||
| 33 | ||||||||||||||||||||||||||||||||||||
| 34 | ||||||||||||||||||||||||||||||||||||
| 35 | ||||||||||||||||||||||||||||||||||||
| 36 | ||||||||||||||||||||||||||||||||||||
| 37 | ||||||||||||||||||||||||||||||||||||
| 38 | ||||||||||||||||||||||||||||||||||||
| 39 | ||||||||||||||||||||||||||||||||||||
| 40 | ||||||||||||||||||||||||||||||||||||
| 41 | ||||||||||||||||||||||||||||||||||||
| 42 | ||||||||||||||||||||||||||||||||||||
| 43 | ||||||||||||||||||||||||||||||||||||
| 44 | ||||||||||||||||||||||||||||||||||||
| 45 | ||||||||||||||||||||||||||||||||||||
| 46 | ||||||||||||||||||||||||||||||||||||
| 47 | ||||||||||||||||||||||||||||||||||||
| 48 | ||||||||||||||||||||||||||||||||||||
| 49 | ||||||||||||||||||||||||||||||||||||
| 50 |
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 plasmid-input DNA barcode counts per million across two input replicates for allele_1.
- allele_2_mean_dna_cpm
- Mean plasmid-input DNA barcode counts per million across two input replicates for allele_2.
- allele_3_mean_dna_cpm
- Mean plasmid-input DNA barcode counts per million across two input replicates for allele_3; blank for biallelic variants.
- allele_1_mean_rna_cpm
- Mean RNA/cDNA reporter barcode counts per million across three RNA replicates for allele_1.
- allele_2_mean_rna_cpm
- Mean RNA/cDNA reporter barcode counts per million across three RNA replicates for allele_2.
- allele_3_mean_rna_cpm
- Mean 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
- true when the variant appears in the publication's 22Rv1 Supplementary Table S6 functional-SNP list; false otherwise.
- min_raw_count
- Minimum raw barcode count across all listed allele barcodes, three RNA replicates, and two 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 plasmid-input files; this retained 209 of 211 mapped SNP IDs and excluded rs1456315 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
This is the MPRA experiment explicitly described in the publication. The paper reports 213 SNPs, while the GEO barcode mapping contains 211 SNP IDs and 425 allele constructs, including three mapped multi-allelic IDs; allele_3 columns preserve those extra constructs. Five mapped IDs have no matching Table S1 annotation and therefore retain blank annotation fields. The paper-reported hit flag is taken directly from Supplementary Table S6; the numeric activity and p-value columns were regenerated from the deposited GEO counts.