T1D enhancer variant MPRA in activated primary human CD4+ T cells
Identification of functional enhancer variants associated with type I diabetes in CD4+ T cellsA synthetic oligonucleotide library tested reference and alternate alleles for 121 T1D-associated enhancer variants in activated primary human CD4+ T cells. The STARR-seq-style episomal reporter was quantified using matched plasmid-DNA and reporter-RNA counts, producing allele-specific enhancer activity estimates.
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
Anti-CD3/anti-CD28 bead activation; IL-2 (10 ng/mL) added at 48 h
The library used synthetic oligonucleotides containing 230-nucleotide genomic regions for the reference and alternate alleles and adopted the pSTARR-seq self-transcribing reporter design. Primary human CD4+ T cells were electroporated after anti-CD3/anti-CD28 activation and IL-2 expansion. Poly-A reporter RNA and plasmid DNA libraries were prepared, sequenced on an Illumina NextSeq 550 with 1 × 75-cycle reads, mapped with Bowtie2, quantified with featureCounts, and analyzed with QuASAR-MPRA. The deposited SRA run metadata contains five DNA and five RNA sequencing runs; the publication does not specify whether these are biological or technical replicates.
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 · 24 definitions
- variant_id
- Enhancer SNP identifier tested in the MPRA.
- lead_snp
- Lead T1D GWAS SNP associated with the enhancer SNP through linkage disequilibrium.
- ld_r2
- Reported squared correlation (RSquared) between the enhancer SNP and lead SNP.
- chromosome
- Chromosome reported for the enhancer SNP.
- start_hg19_0based
- Source chromStart coordinate on hg19, represented as a 0-based start.
- end_hg19_1based
- Source chromEnd coordinate on hg19 for the one-base interval; numerically equal to the 1-based variant position.
- variant_position_hg19
- Derived 1-based hg19 variant position (start_hg19_0based + 1).
- strand
- Reported strand for the enhancer interval.
- reference_allele
- NCBI reference allele used for the reference reporter construct.
- observed_alleles
- Slash-delimited alleles observed at the SNP in the source table; some sites are multiallelic.
- rna_count_ref
- Reported reporter-RNA read count for the reference allele.
- dna_count_ref
- Reported plasmid-DNA read count for the reference allele.
- rna_count_alt
- Reported reporter-RNA read count for the alternate-allele construct.
- dna_count_alt
- Reported plasmid-DNA read count for the alternate-allele construct.
- rna_dna_ratio_ref
- Reporter-RNA count divided by plasmid-DNA count for the reference allele.
- rna_dna_ratio_alt
- Reporter-RNA count divided by plasmid-DNA count for the alternate allele.
- log2_activity_ref
- Log2-transformed RNA/DNA enhancer activity for the reference allele.
- log2_activity_alt
- Log2-transformed RNA/DNA enhancer activity for the alternate allele.
- fold_change_ref_over_alt
- Source fold change, defined as reference activity divided by alternate activity.
- log2_fc_ref_over_alt
- Source log2 fold change for reference activity over alternate activity.
- log2_fc_alt_over_ref
- Derived log2 fold change for alternate activity over reference activity; the negative of log2_fc_ref_over_alt.
- p_value
- Reported p-value for the allele-specific enhancer activity test.
- fdr_bh
- Benjamini-Hochberg adjusted p-value reported by the authors.
- passes_fdr_10pct
- Boolean flag indicating whether fdr_bh is below 0.10, the paper's significance threshold.
Quality control
The paper reports adapter and low-quality read checks with FASTQC (quality score <20), trimming with Trim Galore, Bowtie2 mapping, featureCounts quantification, and QuASAR-MPRA allele-specific analysis. Benjamini-Hochberg adjustment defined significant allelic activity at FDR <10%. For this package, rows were retained only when all MPRA count, ratio, p-value, and FDR fields were present and finite, RNA/DNA counts were nonnegative, and both reference and alternate DNA counts were at least 10. All 121 source rows passed these table-level QC checks (minimum DNA counts: 11 reference and 12 alternate); the four rows with FDR <0.10 are flagged in passes_fdr_10pct, while nonsignificant tested variants remain available for effect-size analyses.
Curation notes
Table_1.xlsx is the authors' aggregate MPRA result table; its unlabeled blank source column was omitted. The processed table contains all 121 complete, QC-passing variants and preserves nonsignificant results. Because the source's observed_alleles field is multiallelic for some SNPs and its RNA_alt/DNA_alt columns do not name a unique alternate base in those rows, the package preserves the reported allele set rather than inferring a single alternate nucleotide. The coordinate fields are hg19 and are represented as a 0-based start, a one-base end coordinate, and a derived 1-based position. Table_2.xlsx, Table_3.xlsx, and the supplementary figures PDF are retained in raw_data for TF-binding and CRISPRi context; sequencing reads are not included. The CRISPRi validation is not represented as a second MPRA experiment because it is a separate gene-expression perturbation assay.