79k allelic MPRA library across LCLs and HepG2
Direct identification of hundreds of expression-modulating variants using a multiplexed reporter assayA 78,956-oligo episomal MPRA library tested reference and alternative alleles for eQTL-linked, GWAS-linked, and control variants in the lymphoblastoid cell lines NA12878 and NA19239 and in HepG2. The table contains the authors' combined-LCL activity and allelic-skew statistics together with count-derived activity summaries for each deposited cell-line condition.
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
Synthetic 180-mer oligos placed approximately 150 bp of genomic sequence around the centered variant upstream of a minimal promoter and GFP reporter. Each oligo was tagged with 20-nucleotide barcodes in the GFP 3' UTR by emulsion PCR; plasmid input and GFP RNA were barcode-sequenced after transfection, with RNA harvested 24 hours post-transfection. The deposited 79k count matrix contains five plasmid-input replicates, five NA12878 RNA replicates, three NA19239 RNA replicates, and five HepG2 RNA replicates. The original analysis used DESeq2 median-of-ratios normalization and negative-binomial modeling, with a separate paired allelic-skew analysis for reference versus alternative alleles.
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 · 52 definitions
- element_id
- Author Table S1 internal ID for one tested reference/alternative pair in a particular neighboring haplotype and oligo orientation.
- variant_id
- Centered variant identifier, usually an rsID or a coordinate-style indel identifier.
- variant_type
- SNP for rsID records; indel_or_coordinate_id for coordinate-style records.
- direction_relative_to_tss
- Author design orientation relative to the target transcription start site: pos or neg.
- neighboring_haplotype
- Author Table S1 haplotype label; ref or alt describes the surrounding sequence at neighboring polymorphisms, while the reference/alternative contrast remains the centered variant contrast.
- reference_oligo_id
- GEO collapsed-count row ID for the centered reference allele (the author's C.A allele).
- alternate_oligo_id
- GEO collapsed-count row ID for the centered alternative allele (the author's C.B allele).
- qc_status
- Package-level status; only records passing the paired plasmid-input threshold are emitted.
- qc_min_dna_count
- Smaller of the reference and alternative summed plasmid-input counts across Plasmid_r1 through Plasmid_r5.
- reference_dna_count_sum
- Sum of the five unnormalized deposited plasmid-input counts for the reference oligo.
- alternate_dna_count_sum
- Sum of the five unnormalized deposited plasmid-input counts for the alternative oligo.
- reference_dna_cpm_mean
- Mean reference plasmid-input count per million across the five plasmid replicates, using each sample's total oligo count for normalization.
- alternate_dna_cpm_mean
- Mean alternative plasmid-input count per million across the five plasmid replicates, using each sample's total oligo count for normalization.
- reference_na12878_rna_count_sum
- Sum of reference oligo counts across the five deposited NA12878 RNA replicates.
- alternate_na12878_rna_count_sum
- Sum of alternative oligo counts across the five deposited NA12878 RNA replicates.
- reference_na12878_rna_cpm_mean
- Mean reference NA12878 RNA count per million across the five RNA replicates.
- alternate_na12878_rna_cpm_mean
- Mean alternative NA12878 RNA count per million across the five RNA replicates.
- reference_na12878_log2_activity
- Derived NA12878 reference activity: log2((RNA CPM mean + 1)/(DNA CPM mean + 1)).
- alternate_na12878_log2_activity
- Derived NA12878 alternative activity: log2((RNA CPM mean + 1)/(DNA CPM mean + 1)).
- na12878_allelic_log2_effect_alt_minus_ref
- Derived NA12878 alternative-minus-reference activity difference on the log2 scale.
- reference_na19239_rna_count_sum
- Sum of reference oligo counts across the three deposited NA19239 RNA replicates.
- alternate_na19239_rna_count_sum
- Sum of alternative oligo counts across the three deposited NA19239 RNA replicates.
- reference_na19239_rna_cpm_mean
- Mean reference NA19239 RNA count per million across the three RNA replicates.
- alternate_na19239_rna_cpm_mean
- Mean alternative NA19239 RNA count per million across the three RNA replicates.
- reference_na19239_log2_activity
- Derived NA19239 reference activity: log2((RNA CPM mean + 1)/(DNA CPM mean + 1)).
- alternate_na19239_log2_activity
- Derived NA19239 alternative activity: log2((RNA CPM mean + 1)/(DNA CPM mean + 1)).
- na19239_allelic_log2_effect_alt_minus_ref
- Derived NA19239 alternative-minus-reference activity difference on the log2 scale.
- reference_hepg2_rna_count_sum
- Sum of reference oligo counts across the five deposited HepG2 RNA replicates.
- alternate_hepg2_rna_count_sum
- Sum of alternative oligo counts across the five deposited HepG2 RNA replicates.
- reference_hepg2_rna_cpm_mean
- Mean reference HepG2 RNA count per million across the five RNA replicates.
- alternate_hepg2_rna_cpm_mean
- Mean alternative HepG2 RNA count per million across the five RNA replicates.
- reference_hepg2_log2_activity
- Derived HepG2 reference activity: log2((RNA CPM mean + 1)/(DNA CPM mean + 1)).
- alternate_hepg2_log2_activity
- Derived HepG2 alternative activity: log2((RNA CPM mean + 1)/(DNA CPM mean + 1)).
- hepg2_allelic_log2_effect_alt_minus_ref
- Derived HepG2 alternative-minus-reference activity difference on the log2 scale.
- reference_combined_lcl_log2_activity
- Derived LCL reference activity, weighted by the deposited replicate counts: five NA12878 replicates and three NA19239 replicates.
- alternate_combined_lcl_log2_activity
- Derived LCL alternative activity, weighted by the deposited replicate counts: five NA12878 replicates and three NA19239 replicates.
- combined_lcl_allelic_log2_effect_alt_minus_ref
- Derived combined-LCL alternative-minus-reference activity difference on the log2 scale.
- published_reference_plasmid_mean
- Author Table S1 C.A.ctrl.mean: normalized plasmid count mean for the reference allele.
- published_reference_rna_mean
- Author Table S1 C.A.exp.mean: RNA count mean for the reference allele.
- published_reference_log2_activity
- Author Table S1 C.A.log2FC: published reference-allele log2 fold change for RNA relative to plasmid input.
- published_reference_logp
- Author Table S1 C.A.logP statistic for reference-allele expression, preserved on the supplied scale.
- published_reference_logpadj
- Author Table S1 C.A.logPadj statistic for reference-allele expression, the supplied multiple-testing-adjusted statistic.
- published_alternate_plasmid_mean
- Author Table S1 C.B.ctrl.mean: normalized plasmid count mean for the alternative allele.
- published_alternate_rna_mean
- Author Table S1 C.B.exp.mean: RNA count mean for the alternative allele.
- published_alternate_log2_activity
- Author Table S1 C.B.log2FC: published alternative-allele log2 fold change for RNA relative to plasmid input.
- published_alternate_logp
- Author Table S1 C.B.logP statistic for alternative-allele expression, preserved on the supplied scale.
- published_alternate_logpadj
- Author Table S1 C.B.logPadj statistic for alternative-allele expression, the supplied multiple-testing-adjusted statistic.
- published_na12878_allelic_log2_skew_alt_vs_ref
- Author Table S1 LogSkew.12878: published NA12878 log2 allelic skew, alternative relative to reference.
- published_na19239_allelic_log2_skew_alt_vs_ref
- Author Table S1 LogSkew.19239: published NA19239 log2 allelic skew, alternative relative to reference.
- published_combined_lcl_allelic_log2_skew_alt_vs_ref
- Author Table S1 LogSkew.Comb: published combined-LCL log2 allelic skew, alternative relative to reference.
- published_combined_lcl_skew_logp
- Author Table S1 C.Skew.logP: published combined-LCL allelic-skew logP statistic.
- published_combined_lcl_skew_fdr
- Author Table S1 C.Skew.fdr: published combined-LCL allelic-skew false-discovery rate.
Quality control
The authors filtered barcode/oligo alignments by adapter and constant-sequence matching, required an oligo-alignment score of at least 0.95, removed conflicting barcode assignments, and aggregated barcode counts by oligo. Their analysis used DESeq2 median-of-ratios normalization, negative-binomial modeling, Bonferroni-corrected expression calls at p <= 0.01, and Benjamini-Hochberg FDR for allelic skew. For this package, the 39,478 complete reference/alternative records in author Table S1 were joined to the GEO collapsed counts and retained only when both alleles had at least 20 summed plasmid-input reads across the five deposited plasmid replicates; 39,124 records passed and 354 low-input records were excluded. Count-derived activity values are per-sample CPM summaries with a 1-count-on-the-CPM-scale pseudocount and are provided alongside, not in place of, the authors' published statistics.
Curation notes
The processed table is one row per author-defined reference/alternative pair record; Haplotype is the authors' neighboring-variant background label, not a second centered allele contrast. The GEO count row suffixes A and B correspond to the reference and alternative centered alleles for the Table S1 records. The deposited matrix has five NA12878, three NA19239, and five HepG2 RNA columns; the main manuscript text gives a different shorthand replicate description in one passage, so the deposited column structure was used. The paper's later correction (10.1016/j.cell.2018.02.021) reverses the reported direction for the PTGER4 rs9283753 validation and corrects the cell line shown in one figure; the packaged count/S1 data are retained as deposited and should be interpreted with that correction in mind.