SH-SY5Y allele-specific episomal MPRA (both batches)
A screen of 1,049 schizophrenia and 30 Alzheimer’s-associated variants for regulatory potentialThe same synthetic variant library was transfected into SH-SY5Y human neuroblastoma cells in six independent transfections across two batches. Each allele was represented by five uniquely barcoded oligonucleotide constructs in a pMPRA1 plasmid reporter; the published combined-batch analysis used ComBat correction before allele-level testing.
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 (plasmid transfection only)
A 95-bp variant-centered synthetic oligonucleotide was cloned into pMPRA1, with a CMV minimal promoter driving GFP and a unique barcode downstream of the reporter. Six independent SH-SY5Y transfections were assayed by 50-bp single-end Illumina MiSeq sequencing of DNA and RNA barcode libraries in two batches; the published combined-batch analysis applied ComBat to log-ratio activity measures and then used total-count normalization and the paired mixed-model mpralm method.
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 · 22 definitions
- variant_id
- dbSNP rs identifier for the assayed variant.
- chromosome
- Chromosome label from the source table.
- position_hg19
- 1-based source SNP coordinate; the paper labels assayed SNP locations as hg19.
- disease
- Source disease group: SCZ (schizophrenia) or ALZ (Alzheimer’s disease).
- assayed_alleles
- Alleles represented in the sequence supplement, separated by |; these are not labeled as reference or risk alleles.
- allele_count
- Number of distinct allele constructs represented in the sequence supplement.
- oligo_construct_count
- Number of sequence-supplement constructs for this variant across all assayed alleles; normally five constructs per allele.
- barcodes_per_allele
- Designed barcode-indexed technical replicates per allele (5).
- tested_region_length_bp
- Length of the variant-centered sequence in the sequence supplement; most are 95 bp and rs159961 is 68 bp.
- analysis_cell_line
- Cell line represented by this experiment table (SH-SY5Y; both batches).
- f_pvalue
- Published raw F-test p-value for differential activity between alleles; it is not an effect-size estimate.
- fdr
- Published multiple-testing-adjusted F-test p-value/FDR for differential allelic activity.
- significant_allelic_activity_fdr_lt_0_05
- TRUE when the published FDR is < 0.05; indicates a significant allelic activity difference but not its direction.
- max_cv_dna_ge5_A
- Maximum CV of RNA/DNA ratios for the A allele after excluding barcodes with fewer than 5 DNA reads; blank means unavailable.
- max_cv_dna_ge5_C
- Maximum CV of RNA/DNA ratios for the C allele after excluding barcodes with fewer than 5 DNA reads; blank means unavailable.
- max_cv_dna_ge5_G
- Maximum CV of RNA/DNA ratios for the G allele after excluding barcodes with fewer than 5 DNA reads; blank means unavailable.
- max_cv_dna_ge5_T
- Maximum CV of RNA/DNA ratios for the T allele after excluding barcodes with fewer than 5 DNA reads; blank means unavailable.
- max_cv_dna_ge10_A
- Maximum CV of RNA/DNA ratios for the A allele after excluding barcodes with fewer than 10 DNA reads; blank means unavailable.
- max_cv_dna_ge10_C
- Maximum CV of RNA/DNA ratios for the C allele after excluding barcodes with fewer than 10 DNA reads; blank means unavailable.
- max_cv_dna_ge10_G
- Maximum CV of RNA/DNA ratios for the G allele after excluding barcodes with fewer than 10 DNA reads; blank means unavailable.
- max_cv_dna_ge10_T
- Maximum CV of RNA/DNA ratios for the T allele after excluding barcodes with fewer than 10 DNA reads; blank means unavailable.
- qc_pass
- TRUE for a row retained after the source successful-assay/statistical-result QC filter.
Quality control
The paper normalized DNA and RNA libraries by total counts, summarized each MPRA element by aggregated barcode counts, and calculated RNA/DNA-ratio coefficient of variation (CV) across the five allele barcodes. Barcodes with fewer than 5 or fewer than 10 DNA reads were omitted from the respective CV calculation, and SNPs with a CV above the 99th-percentile threshold were flagged. The paper included both SH-SY5Y batches in the primary differential analysis after ComBat correction despite lower second-batch activity correlations. For this package, the six Table SS1 rows lacking a SH-SY5Y raw and adjusted F-test p-value (rs1763839, rs1198591, rs9823697, rs72691094, rs6449528, and rs6999792) were filtered because no differential result was available; 1,073 rows remain. Significant allelic activity is represented by the published adjusted F-test p-value/FDR < 0.05.
Curation notes
SH-SY5Y is resolved to Cellosaurus CVCL:0019 (the article gives ATCC CRL-2266). The primary processed table represents the paper’s combined two-batch SH-SY5Y analysis, not a separate batch-2-only sensitivity sheet. Six rows with missing SH-SY5Y F-test p-values/FDR were excluded as not assessable. Table SS1 does not report allele-specific MPRA effect sizes, reference/risk allele labels, or directions, so the processed table intentionally does not infer them. The four additional SNPs present in the sequence supplement but absent from Table SS1 were treated as unsuccessful assays and excluded from the processed table.