K562 allele-specific episomal MPRA
A screen of 1,049 schizophrenia and 30 Alzheimer’s-associated variants for regulatory potentialThe study transfected one synthetic variant library into K-562 chronic myelogenous leukemia cells in three independent transfections. Each tested allele was represented by five uniquely barcoded oligonucleotide constructs in a pMPRA1 plasmid reporter, and DNA/RNA barcode sequencing was used to test differential allelic activity.
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. Three independent K562 transfections were assayed by 50-bp single-end Illumina MiSeq sequencing of DNA and RNA barcode libraries; allele comparisons 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 (K562).
- 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 retained successfully assayed SNPs for differential analysis rather than declaring a hard row-level CV exclusion; this package retains all 1,079 Table SS1 SNP rows with a numeric K562 F-test result and filters no K562 rows. Significant allelic activity is represented by the published adjusted F-test p-value/FDR < 0.05.
Curation notes
K-562 is resolved to Cellosaurus CVCL:0004 (the article gives ATCC CCL-243). 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. Rows with missing per-allele CV values are retained when the paper supplied a differential result because the authors used aggregated barcode counts for the statistical test. 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. The paper’s abstract spells the neuroblastoma line as SK-SY5Y in places, while the methods and cell-line accession identify the line used for this experiment as K562 only.