Experiment / E06TYJKOYEpisomal Plasmid MPRA

79k synthetic MPRA in NA19239 lymphoblastoid cells

Bayesian estimation of genetic regulatory effects in high-throughput reporter assays

Three independent NA19239 transfections of the 78,956-oligo allele library from Tewhey et al. were quantified by barcode-collapsed counts in the plasmid input and reporter RNA. The processed table retains source oligo-pair annotations and computes replicate-normalized RNA/DNA activity and alternate-versus-reference log2 skew for high-coverage variant contexts.

Download processed table (CSV)Raw source data API documentation

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.

Organism: Human
Taxonomy ID: NCBITaxon:9606
Biosample: CVCL:9634
Reference genome: hg19
Design focus: Variant-focused
Region of interest: Not reported / not applicable

Perturbation & assay details

Basal / Untreated

Synthetic 180-bp oligos containing 150 bp of genomic context and adapters were assigned 20-bp barcodes, cloned upstream of a minimal TATA promoter in the mpra-delta-orf/GFP reporter, and measured through barcode abundance in GFP RNA relative to plasmid input. A/B are retained as reference/alternate according to the source Table S1; _RC and _alt labels are retained as source oligo design contexts.

Processed data

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

Visible columns (46 of 46)

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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 · 46 definitions

variant_id: Canonical variant identifier after removing source _RC and _alt context suffixes
oligo_pair_id: Exact GSE75661 Oligo identifier with the terminal A/B allele suffix removed
design_suffix: Source design-context label such as standard, RC, alt, or RC_alt
snp_id: Centered variant identifier from Tewhey Table S1
direction: Oligo direction relative to the target transcription start site from Table S1
haplotype_background: Neighboring-variant sequence background from Table S1: reference or alternative
dna_ref_count: Reference-allele count summed across five plasmid replicates for this oligo pair
dna_alt_count: Alternate-allele count summed across five plasmid replicates for this oligo pair
rna_ref_count: Reference-allele reporter-RNA count summed across three NA19239 replicates for this oligo pair
rna_alt_count: Alternate-allele reporter-RNA count summed across three NA19239 replicates for this oligo pair
dna_total_count: Reference plus alternate plasmid count for this oligo pair
rna_total_count: Reference plus alternate reporter-RNA count for this oligo pair
variant_dna_ref_count: Reference plasmid count summed across all oligo contexts for the canonical variant
variant_dna_alt_count: Alternate plasmid count summed across all oligo contexts for the canonical variant
variant_rna_ref_count: Reference reporter-RNA count summed across all oligo contexts for the canonical variant
variant_rna_alt_count: Alternate reporter-RNA count summed across all oligo contexts for the canonical variant
variant_dna_total_count: Total plasmid count across all contexts and alleles for the canonical variant
variant_rna_total_count: Total reporter-RNA count across all contexts and alleles for the canonical variant
oligo_pair_count_for_variant: Number of source oligo pairs representing the canonical variant
dna_ref_mean_cpm: Mean reference plasmid abundance across replicates, normalized to counts per million
dna_alt_mean_cpm: Mean alternate plasmid abundance across replicates, normalized to counts per million
rna_ref_mean_cpm: Mean reference reporter-RNA abundance across replicates, normalized to counts per million
rna_alt_mean_cpm: Mean alternate reporter-RNA abundance across replicates, normalized to counts per million
log2_activity_ref: Log2 reference reporter-RNA CPM divided by reference plasmid CPM, using a 0.5-CPM pseudocount
log2_activity_alt: Log2 alternate reporter-RNA CPM divided by alternate plasmid CPM, using a 0.5-CPM pseudocount
log2_allelic_skew_alt_vs_ref: Alternate log2 activity minus reference log2 activity
published_log2_skew_this_cell: Published Table S1 alternate-versus-reference log2 skew for NA19239
published_log2_skew_combined: Published Table S1 combined-LCL alternate-versus-reference log2 skew
published_skew_fdr: Published Table S1 combined-LCL FDR for allelic skew
qc_pass: True for rows retained after the documented variant- and pair-level coverage filters
dna_ref_r1: Reference plasmid count in DNA replicate 1
dna_ref_r2: Reference plasmid count in DNA replicate 2
dna_ref_r3: Reference plasmid count in DNA replicate 3
dna_ref_r4: Reference plasmid count in DNA replicate 4
dna_ref_r5: Reference plasmid count in DNA replicate 5
dna_alt_r1: Alternate plasmid count in DNA replicate 1
dna_alt_r2: Alternate plasmid count in DNA replicate 2
dna_alt_r3: Alternate plasmid count in DNA replicate 3
dna_alt_r4: Alternate plasmid count in DNA replicate 4
dna_alt_r5: Alternate plasmid count in DNA replicate 5
rna_ref_r1: Reference reporter-RNA count in NA19239 replicate 1
rna_ref_r2: Reference reporter-RNA count in NA19239 replicate 2
rna_ref_r3: Reference reporter-RNA count in NA19239 replicate 3
rna_alt_r1: Alternate reporter-RNA count in NA19239 replicate 1
rna_alt_r2: Alternate reporter-RNA count in NA19239 replicate 2
rna_alt_r3: Alternate reporter-RNA count in NA19239 replicate 3

Quality control

Filtered to canonical variants with at least 10,000 summed DNA reads and 10,000 summed RNA reads across the relevant replicates and at least 10 reads for each reference/alternate allele in both DNA and RNA, following the BIRD supplement's Tewhey high-coverage benchmark. Each retained oligo-pair context was additionally required to have at least 10 counts for each allele in DNA and RNA. The supplement also mentions MAF >=1%, but MAF is absent from the compact GEO count matrix and was not inferred. All retained rows have qc_pass=true.

Curation notes

This is the public Tewhey et al. GSE75661 benchmark reanalyzed by Majoros et al., not a new LCL transfection from the BIRD paper. The table has one row per retained reference/alternate oligo pair, including multiple source contexts for some canonical variants. Tewhey Table S1 values are included as cross-reference; the newly calculated activity values use the compact unnormalized GEO count matrix.

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