3T3-L1 preadipocyte MPRA of FTO obesity-associated variants
Extensive pleiotropism and allelic heterogeneity mediate metabolic effects of IRX3 and IRX5A biallelic library of 87 common FTO-locus variants in high LD with rs1558902 was tested in mouse 3T3-L1 preadipocytes using an episomal plasmid MPRA. This processed table retains the 21 variants that the authors reported as enhancer-active in at least three assay replicates and flags the five reported allele-specific enhancer effects.
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
Each allele was represented by a 175-bp human genomic fragment with 18-19 unique 10-bp barcodes in the pMPRA1 plasmid (Addgene #49349); a minimal promoter/truncated eGFP spacer separated the enhancer insert and barcode. At least 10 million cells were transfected per replicate, mRNA was converted to cDNA, and indexed 50-nt paired-end HiSeq 4000 sequencing measured input DNA and reporter RNA barcode abundance. Authors used two soft biological replicates, each with two technical replicates.
Processed data
50 rows per page. Click a cell to inspect its full value.
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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 · 18 definitions
- variant_id
- dbSNP identifier for the tested biallelic variant.
- lead_snp
- Lead obesity GWAS SNP used to define the LD set.
- chromosome
- Human chromosome in the hg19 coordinate system.
- start_hg19_0based
- Source Table S3 start coordinate, retained as a zero-based BED-style interval start.
- end_hg19_0based_exclusive
- Source Table S3 end coordinate, retained as the exclusive BED-style interval end.
- position_hg19_1based
- Derived one-based SNP position (start_hg19_0based + 1).
- library_context_bp
- Length of native human sequence synthesized around each allele (175 bp).
- alleles_tested
- Number of synthesized alleles per SNP (biallelic; 2).
- designed_barcodes_per_allele
- Number of unique 10-bp barcodes designed for each allele (18-19).
- library_variants_tested
- Total number of common high-LD variants in the MPRA library (87).
- enhancer_activity_detected
- TRUE because the authors’ Table S3 cell-line sheet reports enhancer activity for the variant in this cell line.
- minimum_replicates_with_enhancer_activity
- Minimum number of assay replicates supporting the author’s enhancer call (at least 3).
- allele_specific_effect_significant_in_3T3L1
- TRUE if Table S4 marks this variant as a significant allele-specific enhancer-modulating variant in 3T3-L1; otherwise FALSE.
- allele_specific_effect_significant_in_HT22
- TRUE if Table S4 marks this variant as significant in HT22; otherwise FALSE.
- allele_specific_effect_significant_in_this_experiment
- Cell-line-specific allele-effect flag selected from the corresponding Table S4 column.
- luciferase_validation_reported
- TRUE when embedded Table S5 marks this MPRA variant as validated by luciferase; otherwise FALSE.
- source_tables
- Paper supplementary tables from which the row’s calls and annotations were assembled.
- qc_pass
- TRUE for rows retained after applying the authors’ reported barcode/replicate QC and active-enhancer result criterion.
Quality control
Authors retained exact matches to synthesized barcodes, removed low-expression barcodes, required at least 7 unique barcodes per allele for enhancer testing, quantile-normalized barcode activity, and called enhancer activity with a one-tailed Mann-Whitney U test at FDR <5%. Allele-specific effects were tested with a two-sided Mann-Whitney U test at FDR <5%. The source Table S3 active sheet requires enhancer activity in at least three replicates; the processed table retains its cell-line-specific active variants and marks every retained row qc_pass=TRUE. The other tested variants are not included because the open supplement provides no quantitative barcode-level result for them; their omission is not treated as a QC failure.
Curation notes
The paper’s assay datasets are two soft biological replicates × two technical replicates, not four independent biological replicates. This package contains the authors’ categorical active-enhancer and allele-specific calls from Tables S3/S4; numeric barcode-level activity scores, p-values, allele directions, DNA/RNA counts, and exact surviving barcode counts are not present in the open supplemental files. All five MPRA EMVars in Table S4 are flagged in the 3T3-L1 experiment. Table S5 marks rs11075992 and rs9922619 as luciferase-validated MPRA variants. Source table start/end are retained as BED-style hg19 coordinates; position_hg19_1based is derived as start+1.