Experiment / E4F0CDD46Episomal Plasmid MPRA

Combined three-cell-line episomal MPRA of NSCLC candidate variants

Massively parallel variant-to-function mapping determines functional regulatory variants of non-small cell lung cancer

A barcoded, allele-paired library of 120-bp GRCh37 sequences tested transcriptional regulatory effects for NSCLC-associated candidate variants in A549, NCI-H1299, and BEAS-2B cells. The table reports the authors' combined variant-level element-activity and allelic-effect results, with cell type included as a categorical covariate in the nested fixed model.

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: Not reported / not applicable
Reference genome: GRCh37
Design focus: Variant-focused
Region of interest: Not reported / not applicable

Perturbation & assay details

Basal / Untreated

The pMPRA1_Δorf plasmid library contained reference and alternate 120-bp GRCh37 oligos with 15-bp adapters, random 20-bp barcodes, forward and reverse-complement orientations, and scrambled core-sequence controls. A minP:luciferase reporter was inserted before transfection; plasmid-DNA and reporter-cDNA barcodes were sequenced with 2 × 150-bp Illumina NovaSeq chemistry across the three cell lines and six independent replicates, then modeled with a DESeq2 nested fixed model adjusted for cell type.

Processed data

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

Visible columns (33 of 33)

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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 · 33 definitions

variant_id: Source variant identifier in chromosome:position:reference:alternate format.
chromosome: Chromosome from the source variant identifier.
position_grch37: Variant position on GRCh37.
reference_allele: Reference allele from the source variant identifier.
alternate_allele: Alternate allele from the source variant identifier.
rs_id: dbSNP identifier reported for the 82 author-defined frVars; blank when not reported.
frvar_locus: GWAS locus reported for an author-defined frVar; blank for other evaluated variants.
ref_oligo_sequence: Adapter-flanked forward reference oligo sequence supplied in Supplementary Data 1.
alt_oligo_sequence: Adapter-flanked forward alternate oligo sequence supplied in Supplementary Data 1.
ref_oligo_length: Length in bases of the supplied forward reference oligo sequence.
alt_oligo_length: Length in bases of the supplied forward alternate oligo sequence.
expression_log2_fold_change: Source Data Fig2a log2 fold-change for element transcriptional activity, combined across cell types.
expression_padj: Source Data Fig2a Benjamini-Hochberg adjusted P value for element activity.
element_activity_call: Derived call: active or repressed when expression_padj < 0.01, otherwise not_significant.
allelic_log2_fold_change: Source Data Fig2d log2 allelic effect size for alternate relative to reference activity.
allelic_padj: Source Data Fig2d Benjamini-Hochberg adjusted P value for the allelic effect.
allelic_effect_direction: Derived direction of the alternate allele relative to the reference allele.
lung_eqtl_genes: Lung eQTL genes from Source Data Fig2e-2f (NMU_Lung_eqtl_gene).
frvar_annotated_eqtl_genes: Annotated eQTL genes listed for the frVar in Supplementary Data 2.
chromhmm_A549: A549 ChromHMM core state from Source Data Fig2e-2f.
chromhmm_IMR90: IMR90 ChromHMM core state from Source Data Fig2e-2f.
chromhmm_NHLF: Normal human lung fibroblast ChromHMM core state from Source Data Fig2e-2f.
chromhmm_fetal_lung: Fetal-lung ChromHMM core state from Source Data Fig2e-2f.
chromhmm_lung: Lung ChromHMM core state from Source Data Fig2e-2f.
tfbs_hocomoco: Predicted transcription-factor binding site annotation from HOCOMOCO.
tfbs_jaspar: Predicted transcription-factor binding site annotation from JASPAR.
encode_atac_dnase_overlap: Binary overlap tag for lung-related ENCODE ATAC/DNase annotations.
encode_H3K27ac_overlap: Binary overlap tag for lung-related ENCODE H3K27ac annotations.
encode_H3K4me3_overlap: Binary overlap tag for lung-related ENCODE H3K4me3 annotations.
encode_H3K4me1_overlap: Binary overlap tag for lung-related ENCODE H3K4me1 annotations.
lungenn_max_feature_difference: Maximum LungENN predicted functional difference score across modeled lung features.
is_frvar: True for the 82 author-defined functional regulatory variants listed in Supplementary Data 2.
qc_pass: True for rows retained from the authors' final QC-passed 1,249-variant source result set.

Quality control

The authors merged paired-end reads with FLASH, uniquely aligned reads with STAR, removed low-quality alignments and barcode-oligo mappings detected on multiple oligos, clustered barcode errors with Bartender, and aggregated exact barcode-to-oligo counts. Oligos were retained only when activity measurements were available from at least five unique barcodes and the mean raw count was at least 150 across all samples. The final source result set contains 2,383 allelic pairs from 1,249 variants; the processed table retains those 1,249 source-result variants, requires a matching row in each MPRA source-data view and one unique forward reference/alternate sequence in Supplementary Data 1, and excludes the 39 designed variants absent from the final result set.

Curation notes

This is one combined experiment because the released MPRA summary statistics are modeled across A549 (CVCL:0023), NCI-H1299 (CVCL:0060), and BEAS-2B (CVCL:0168), rather than providing separate cell-line-specific result columns. biosample_id is therefore null instead of assigning the aggregate result to one cell line. The paper describes the six replicates as independent technical replicates in the Results and biological replicates in the Methods; that wording discrepancy is preserved here. The table is variant-level and includes the forward reference/alternate sequences, not barcode-level counts or raw FASTQ reads.

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