HT22 hippocampal neuronal 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 HT22 hippocampal neuronal cells using an episomal plasmid MPRA. This processed table retains the 18 variants that the authors reported as enhancer-active in at least three assay replicates and flags the three 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.
Visible columns (18 of 18)
| Row | ||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | ||||||||||||||||||
| 2 | ||||||||||||||||||
| 3 | ||||||||||||||||||
| 4 | ||||||||||||||||||
| 5 | ||||||||||||||||||
| 6 | ||||||||||||||||||
| 7 | ||||||||||||||||||
| 8 | ||||||||||||||||||
| 9 | ||||||||||||||||||
| 10 | ||||||||||||||||||
| 11 | ||||||||||||||||||
| 12 | ||||||||||||||||||
| 13 | ||||||||||||||||||
| 14 | ||||||||||||||||||
| 15 | ||||||||||||||||||
| 16 | ||||||||||||||||||
| 17 | ||||||||||||||||||
| 18 |
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. The HT22 MPRA EMVars in Table S4 are rs11075992, rs62033403, and rs9940128; rs9922619 and rs9937709 are 3T3-L1-only. 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.