MIN6 episomal MPRA under DMSO vehicle control
Functional characterization of T2D-associated SNP effects on baseline and ER stress-responsive β cell transcriptional activationThe library tested 200-bp human genomic sequences centered on 6,621 candidate SNPs/indels, with reference and alternate alleles represented by barcoded GFP reporter constructs. This arm used MIN6 mouse β cells exposed to 0.025% DMSO vehicle for 24 hours after transfection, with five paired biological replicates and plasmid-DNA/RNA barcode readout.
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
0.025% DMSO vehicle control for 24 h
Each 200-bp human sequence was cloned upstream of a minimal TATA promoter driving GFP, and each construct carried a unique 20-bp barcode in the GFP 3′ UTR. The episomal plasmid library was transfected into MIN6 mouse β cells with Lipofectamine 2000; plasmid-DNA input and captured GFP-mRNA barcode counts were sequenced, with MPRA activity reported as log2 RNA/DNA. The DMSO arm used the second library batch and five paired biological replicates; GEO provides separate DMSO/Tg count matrices for Run1 and Run2, while this table uses the authors' consolidated SNP-level results.
Processed data
50 rows per page. Click a cell to inspect its full value.
Visible columns (43 of 43)
| Row | |||||||||||||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | |||||||||||||||||||||||||||||||||||||||||||
| 2 | |||||||||||||||||||||||||||||||||||||||||||
| 3 | |||||||||||||||||||||||||||||||||||||||||||
| 4 | |||||||||||||||||||||||||||||||||||||||||||
| 5 | |||||||||||||||||||||||||||||||||||||||||||
| 6 | |||||||||||||||||||||||||||||||||||||||||||
| 7 | |||||||||||||||||||||||||||||||||||||||||||
| 8 | |||||||||||||||||||||||||||||||||||||||||||
| 9 | |||||||||||||||||||||||||||||||||||||||||||
| 10 | |||||||||||||||||||||||||||||||||||||||||||
| 11 | |||||||||||||||||||||||||||||||||||||||||||
| 12 | |||||||||||||||||||||||||||||||||||||||||||
| 13 | |||||||||||||||||||||||||||||||||||||||||||
| 14 | |||||||||||||||||||||||||||||||||||||||||||
| 15 | |||||||||||||||||||||||||||||||||||||||||||
| 16 | |||||||||||||||||||||||||||||||||||||||||||
| 17 | |||||||||||||||||||||||||||||||||||||||||||
| 18 | |||||||||||||||||||||||||||||||||||||||||||
| 19 | |||||||||||||||||||||||||||||||||||||||||||
| 20 | |||||||||||||||||||||||||||||||||||||||||||
| 21 | |||||||||||||||||||||||||||||||||||||||||||
| 22 | |||||||||||||||||||||||||||||||||||||||||||
| 23 | |||||||||||||||||||||||||||||||||||||||||||
| 24 | |||||||||||||||||||||||||||||||||||||||||||
| 25 | |||||||||||||||||||||||||||||||||||||||||||
| 26 | |||||||||||||||||||||||||||||||||||||||||||
| 27 | |||||||||||||||||||||||||||||||||||||||||||
| 28 | |||||||||||||||||||||||||||||||||||||||||||
| 29 | |||||||||||||||||||||||||||||||||||||||||||
| 30 | |||||||||||||||||||||||||||||||||||||||||||
| 31 | |||||||||||||||||||||||||||||||||||||||||||
| 32 | |||||||||||||||||||||||||||||||||||||||||||
| 33 | |||||||||||||||||||||||||||||||||||||||||||
| 34 | |||||||||||||||||||||||||||||||||||||||||||
| 35 | |||||||||||||||||||||||||||||||||||||||||||
| 36 | |||||||||||||||||||||||||||||||||||||||||||
| 37 | |||||||||||||||||||||||||||||||||||||||||||
| 38 | |||||||||||||||||||||||||||||||||||||||||||
| 39 | |||||||||||||||||||||||||||||||||||||||||||
| 40 | |||||||||||||||||||||||||||||||||||||||||||
| 41 | |||||||||||||||||||||||||||||||||||||||||||
| 42 | |||||||||||||||||||||||||||||||||||||||||||
| 43 | |||||||||||||||||||||||||||||||||||||||||||
| 44 | |||||||||||||||||||||||||||||||||||||||||||
| 45 | |||||||||||||||||||||||||||||||||||||||||||
| 46 | |||||||||||||||||||||||||||||||||||||||||||
| 47 | |||||||||||||||||||||||||||||||||||||||||||
| 48 | |||||||||||||||||||||||||||||||||||||||||||
| 49 | |||||||||||||||||||||||||||||||||||||||||||
| 50 |
Filters apply to this table only. The CSV download contains the complete processed table; filtered rows are available through the API.
Column dictionary · 43 definitions
- variant_id
- dbSNP identifier for the tested SNP or indel.
- chromosome
- Human chromosome in the hg19 assembly.
- position_hg19
- 1-based hg19 coordinate of the tested variant.
- ref_allele
- Reference allele used in the reporter construct; indel alleles may contain multiple bases.
- alt_allele
- Alternate allele used in the reporter construct; indel alleles may contain multiple bases.
- maf_african
- Minor-allele frequency in the African population.
- maf_american
- Minor-allele frequency in the American population.
- maf_asian
- Minor-allele frequency in the Asian population.
- maf_european
- Minor-allele frequency in the European population.
- caqtl
- Binary flag indicating an islet chromatin-accessibility QTL SNP.
- not_caqtl
- Binary flag indicating an islet ATAC-seq control SNP that was not a caQTL.
- t2d_associated
- Binary flag indicating membership in the T2D-associated SNP/indel set.
- islet_atac_peak
- Binary flag for overlap with a human islet ATAC-seq peak.
- islet_pdx1_peak
- Binary flag for overlap with a human islet PDX1 ChIP-seq peak.
- islet_foxa2_peak
- Binary flag for overlap with a human islet FOXA2 ChIP-seq peak.
- islet_h2az_peak
- Binary flag for overlap with a human islet H2A.Z ChIP-seq peak.
- islet_h3k27ac_peak
- Binary flag for overlap with a human islet H3K27ac ChIP-seq peak.
- islet_mafb_peak
- Binary flag for overlap with a human islet MAFB ChIP-seq peak.
- islet_nkx61_peak
- Binary flag for overlap with a human islet NKX6.1 ChIP-seq peak.
- islet_ctcf_peak
- Binary flag for overlap with a human islet CTCF ChIP-seq peak.
- overlaps_line
- Binary flag for overlap with a RepeatMasker LINE element.
- overlaps_ltr
- Binary flag for overlap with a RepeatMasker LTR element.
- overlaps_sine
- Binary flag for overlap with a RepeatMasker SINE element.
- overlaps_satellite
- Binary flag for overlap with a satellite repeat.
- overlaps_simple_repeat
- Binary flag for overlap with a simple repeat.
- higher_activity_allele
- Allele reported as significantly higher in the reference-versus-alternate comparison; blank when not significant or not reported.
- ref_plasmid_representation_mean
- Author median-normalized mean plasmid-DNA representation for the reference allele.
- ref_activity_log2_rna_dna
- Reference-allele log2 fold change of RNA barcode counts versus plasmid-DNA input.
- ref_activity_pvalue
- Reference-allele p-value for the RNA-versus-plasmid activity test.
- ref_activity_padj
- Reference-allele multiple-testing-adjusted activity p-value.
- ref_enhancer_call
- Reference-allele MPRA activity call: 1 = active at FDR < 1%, 0 = not active.
- alt_plasmid_representation_mean
- Author median-normalized mean plasmid-DNA representation for the alternate allele.
- alt_activity_log2_rna_dna
- Alternate-allele log2 fold change of RNA barcode counts versus plasmid-DNA input.
- alt_activity_pvalue
- Alternate-allele p-value for the RNA-versus-plasmid activity test.
- alt_activity_padj
- Alternate-allele multiple-testing-adjusted activity p-value.
- alt_enhancer_call
- Alternate-allele MPRA activity call: 1 = active at FDR < 1%, 0 = not active.
- active_allele_count
- Number of the two tested alleles with an MPRA activity call of 1.
- allelic_effect_log2_alt_over_ref
- Author log2 fold change of alternate-versus-reference MPRA activity.
- allelic_effect_t_statistic
- Paired t-statistic for the alternate-versus-reference log-transformed RNA/DNA comparison.
- allelic_effect_pvalue
- P-value for the paired alternate-versus-reference allelic comparison.
- allelic_effect_fdr
- FDR for the allelic comparison; blank when the source used -1 to indicate not tested.
- allelic_effect_tested
- 1 when an allelic-skew test was reported, 0 when it was not tested.
- allelic_effect_significant_fdr_10pct
- Allelic-skew call: 1 = FDR < 10%, 0 = tested but not significant, blank = not tested.
Quality control
The authors discarded barcodes mapping to more than one sequence, summed barcode counts within replicates, median-normalized the counts, called sequence activity with a DESeq2 negative-binomial model at FDR < 1%, and tested reference-versus-alternate allelic skew with paired t-tests at FDR < 10%. Supplementary Figure 1 reports strong replicate correlation and PCA separation of RNA from plasmid input. For this package, 6,487 of 6,621 SNP rows were retained because both alleles had numeric plasmid representation, activity p-value/padj, and enhancer-call fields in the source table; 134 rows with no condition-level values were excluded. Non-significant measured variants remain as valid negative results; source -1 allelic-skew sentinels are represented by blank FDR with allelic_effect_tested = 0.
Curation notes
The human inserts were assayed in mouse MIN6 cells (Cellosaurus CVCL:0431); hg19 coordinates and human islet annotations are retained as reported. This DMSO vehicle arm is paired with the thapsigargin arm in the second library batch; the paper does not directly compare this batch with the separate standard-culture batch. The table is a SNP-level extraction of Supplementary Data 3 (MOESM5); both GEO DMSO/Tg count matrices and the oligo/probe FASTA are retained in raw_data.