Experiment / E8SJAY1UBEpisomal Plasmid MPRA

HT22 hippocampal neuron MPRA

A functional genomics pipeline identifies pleiotropy and cross-tissue effects within obesity-associated GWAS loci

An episomal pMPRA1 library of 175-bp human genomic sequences centered on 2,396 high-LD BMI GWAS SNPs was tested in the mouse HT22 hippocampal neuronal cell line. The table contains the 85 study-level EMVars with at least one reported activity value across two biological libraries and the available technical replicates (three for biological replicate 1 and two for biological replicate 2).

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: Mouse
Taxonomy ID: NCBITaxon:10090
Biosample: CVCL:0321
Reference genome: hg19
Design focus: Variant-focused
Region of interest: Not reported / not applicable

Perturbation & assay details

Basal / untreated HT22 cells; cells collected 48 h after transfection

The pMPRA1 episomal reporter contained 175 bp of endogenous human sequence centered on each candidate SNP and 18–19 unique 10-bp barcodes per allele. Reporter RNA activity was measured against input plasmid DNA after transfection; the paper reports quantile-normalized activity units. The source replicate structure is two independently cloned biological libraries with three technical transfections for biological replicate 1 and two technical transfections for biological replicate 2 in this condition.

Processed data

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

Visible columns (24 of 24)

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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

rs_id: dbSNP rs identifier for the enhancer-modulating variant.
chromosome: Chromosome reported in Supplementary Data 6.
start_hg19_0based: 0-based half-open interval start in hg19 from Supplementary Data 6.
end_hg19_0based_exclusive: 0-based half-open interval end in hg19 from Supplementary Data 6.
coordinate_hg19: Compact source coordinate in the form chromosome:start-end.
lead_snp: BMI GWAS lead SNP linked to rs_id in Supplementary Data 3.
r2_with_lead_snp: CEU r-squared between rs_id and the linked lead SNP from Supplementary Data 3.
maf_ceu: CEU minor-allele frequency from Supplementary Data 3.
distance_to_lead_bp: Absolute distance in base pairs from rs_id to the linked lead SNP from Supplementary Data 3.
adipose_mpra_enhancer: True if rs_id appears in the study's adipose MPRA enhancer set, Supplementary Data 4.
brain_mpra_enhancer: True if rs_id appears in the study's brain MPRA enhancer set, Supplementary Data 5.
source_emvar: True for every row; rs_id appears in the study-level EMVar activity sheet, Supplementary Data 6.
activity_biorep1_tech1: Source Supplementary Data 6 MPRA activity unit for biological replicate 1, technical replicate 1; blank means the source reported NA.
activity_biorep1_tech2: Source Supplementary Data 6 MPRA activity unit for biological replicate 1, technical replicate 2; blank means the source reported NA.
activity_biorep1_tech3: Source Supplementary Data 6 MPRA activity unit for biological replicate 1, technical replicate 3; blank means the source reported NA.
activity_biorep2_tech1: Source Supplementary Data 6 MPRA activity unit for biological replicate 2, technical replicate 1; blank means the source reported NA.
activity_biorep2_tech2: Source Supplementary Data 6 MPRA activity unit for biological replicate 2, technical replicate 2; blank means the source reported NA.
activity_biorep1_mean: Arithmetic mean of available source activity units in biological replicate 1.
activity_biorep2_mean: Arithmetic mean of available source activity units in biological replicate 2.
activity_mean: Arithmetic mean of all available source activity units for this variant and condition.
activity_median: Median of all available source activity units for this variant and condition.
activity_sd: Sample standard deviation of all available source activity units; blank when fewer than two values were reported.
n_observed_replicates: Number of non-NA source activity values used in the summaries.
qc_status: Pass: variant is in the paper's post-QC EMVar sheet and has at least one source activity value in this condition.

Quality control

The paper required exact reverse-complement matches to expected barcodes, removed lowly expressed barcodes, required at least 8 CT enrichment of eGFP RT(+) over RT(−) to limit plasmid-DNA contamination, and called EMVars using FDR-corrected two-sided Mann–Whitney tests with reproducibility in at least half of technical replicates or both biological replicates. Supplementary Data 6 is the paper's post-QC EMVar activity sheet; rows with no reported activity value for this condition were excluded from this table.

Curation notes

The processed table is a condition-specific view of the 94 study-level EMVars in Supplementary Data 6. The source activity sheet has no allele column, so no nucleotide identity, reference/alternate assignment, or direction of allelic effect was inferred. Source activity units were retained and summarized without recomputing from sequence reads; the source coordinates use hg19 0-based half-open intervals.

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