Allele-specific MPRA in stimulated primary CD4 T cells

The RSV-promoter episomal barcode MPRA tested three overlapping 114-bp reference/alternate constructs per candidate SNP, together with synthetic and genomic controls, in stimulated primary CD4 T cells from 12 healthy donors. This table contains the authors' QuASAR-MPRA fixed-effect meta-analysis results from Dataset EV3, joined to the corresponding library sequences and coordinates.

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: CL:0000624
Reference genome: hg19
Design focus: Variant-focused
Region of interest: Not reported / not applicable

Perturbation & assay details

Four-day stimulation with 10 ng/ml IL-2 and anti-CD2/3/28 bead particles; assayed 24 h after nucleofection

An adapted plasmid MPRA used the Rous sarcoma virus (RSV) promoter and an EGFP reporter. Each 114-bp oligonucleotide was linked to an 11-nt barcode; the library was nucleofected into activated primary CD4 T cells, RNA was collected 24 hours later, and RNA barcode counts were normalized to the input plasmid DNA library. Three overlapping constructs were made for each reference/alternate SNP allele, with additional risk-allele combinations and controls.

Quality control

FastQC was applied to the sequencing data. A barcode was counted only when it exactly matched a library barcode and was followed by at least 10 bases of the expected constant sequence; successful transfection required at least 70% of the barcode library to be represented. Counts were CPM-normalized, barcodes with median CPM <0.5 in RNA or DNA were removed, identical constructs were summed, and construct counts were quantile-normalized. For SNP effects, enhancer constructs were excluded, 964/970 SNP constructs remained, replicate estimates were combined by fixed-effect meta-analysis in QuASAR-MPRA, and Benjamini-Hochberg FDR correction was applied. All table rows are from the authors' post-QC Dataset EV3; non-significant constructs are retained.

Curation notes

The table contains 964 SNP/control constructs from Dataset EV3. Library sequence annotations were joined by construct ID and, for the three coordinate-only 6:14734341 constructs, by exact genomic interval and tile. The supplied beta, odds ratio, P value, q value, and DNA proportion are preserved from the supplementary workbook; non-significant rows remain available for downstream thresholding. The paper also tested the same library in Jurkat cells, which is packaged as a separate child experiment.

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Allele-specific MPRA in stimulated primary CD4 T cells

Processed data

Quality control

Curation notes

Cite OpenMPRA

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