ATRA-versus-vehicle response MPRA of psychiatric risk SNPs in Neuro-2a cells
Transcriptional-regulatory convergence across functional MDD risk variants identified by massively parallel reporter assaysThe same pooled allele/barcode plasmid library was transfected into Neuro-2a cells and assayed after exposure to 20 µM all-trans retinoic acid (ATRA) or vehicle (100% DMSO). Six biological replicates were collected for each condition, enabling allele, drug, and allele-by-drug interaction analysis.
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
20 µM all-trans retinoic acid (ATRA) versus vehicle (100% DMSO), with media refreshed every 24 h
Episomal plasmid MPRA using up to 126-bp human hg19 SNP-centered allele tiles, ten unique 10-bp barcodes per allele, an hsp68 minimal promoter driving dsRed, and a WPRE RNA-stabilization element. Twelve Neuro-2a wells were transfected with the pooled library; six received 20 µM ATRA and six received vehicle. Targeted reporter-barcode RNA and input-plasmid DNA sequencing produced barcode-level log2 RNA/DNA expression values. The authors modeled barcode expression as allele + treatment + allele:treatment with replicate as a random effect.
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 · 68 definitions
- variant_id
- dbSNP rs identifier for the tested SNP.
- source_locus
- GWAS or control locus label associated with the library element.
- ld_block
- Source LD-block identifier for the SNP.
- tag_snp
- GWAS index/tag SNP for the LD block.
- reference_allele
- dbSNP reference allele used for the allele contrast.
- alternate_allele
- dbSNP alternative allele used for the allele contrast.
- sequence_alleles
- Allele pair recorded in the library design sheet.
- maf
- Minor allele frequency recorded in the library design sheet.
- ld_r2
- LD R2 to the tag SNP recorded in the library design sheet.
- snp_hg19_coord
- SNP coordinate in hg19 notation.
- hg38_chromosome
- Chromosome label supplied by the source annotation; coordinates are the source hg38 fields.
- hg38_start
- Source hg38 start coordinate.
- hg38_end
- Source hg38 end coordinate.
- ref_vehicle_barcode_n_after_qc
- Reference barcodes contributing at least one post-QC vehicle expression value.
- alt_vehicle_barcode_n_after_qc
- Alternate barcodes contributing at least one post-QC vehicle expression value.
- ref_atra_barcode_n_after_qc
- Reference barcodes contributing at least one post-QC ATRA expression value.
- alt_atra_barcode_n_after_qc
- Alternate barcodes contributing at least one post-QC ATRA expression value.
- qc_valid_barcode_condition_values
- Number of nonmissing barcode-by-condition expression values among the 240 expected LMM inputs.
- qc_missing_barcode_condition_values
- Number of missing barcode-by-condition expression values among the 240 expected LMM inputs.
- vehicle_ref_activity_rep1
- Basal-normalized mean log2 RNA/DNA activity for the reference allele in vehicle replicate 1.
- vehicle_alt_activity_rep1
- Basal-normalized mean log2 RNA/DNA activity for the alternate allele in vehicle replicate 1.
- vehicle_ref_activity_rep2
- Basal-normalized mean log2 RNA/DNA activity for the reference allele in vehicle replicate 2.
- vehicle_alt_activity_rep2
- Basal-normalized mean log2 RNA/DNA activity for the alternate allele in vehicle replicate 2.
- vehicle_ref_activity_rep3
- Basal-normalized mean log2 RNA/DNA activity for the reference allele in vehicle replicate 3.
- vehicle_alt_activity_rep3
- Basal-normalized mean log2 RNA/DNA activity for the alternate allele in vehicle replicate 3.
- vehicle_ref_activity_rep4
- Basal-normalized mean log2 RNA/DNA activity for the reference allele in vehicle replicate 4.
- vehicle_alt_activity_rep4
- Basal-normalized mean log2 RNA/DNA activity for the alternate allele in vehicle replicate 4.
- vehicle_ref_activity_rep5
- Basal-normalized mean log2 RNA/DNA activity for the reference allele in vehicle replicate 5.
- vehicle_alt_activity_rep5
- Basal-normalized mean log2 RNA/DNA activity for the alternate allele in vehicle replicate 5.
- vehicle_ref_activity_rep6
- Basal-normalized mean log2 RNA/DNA activity for the reference allele in vehicle replicate 6.
- vehicle_alt_activity_rep6
- Basal-normalized mean log2 RNA/DNA activity for the alternate allele in vehicle replicate 6.
- atra_ref_activity_rep1
- Basal-normalized mean log2 RNA/DNA activity for the reference allele in ATRA replicate 1.
- atra_alt_activity_rep1
- Basal-normalized mean log2 RNA/DNA activity for the alternate allele in ATRA replicate 1.
- atra_ref_activity_rep2
- Basal-normalized mean log2 RNA/DNA activity for the reference allele in ATRA replicate 2.
- atra_alt_activity_rep2
- Basal-normalized mean log2 RNA/DNA activity for the alternate allele in ATRA replicate 2.
- atra_ref_activity_rep3
- Basal-normalized mean log2 RNA/DNA activity for the reference allele in ATRA replicate 3.
- atra_alt_activity_rep3
- Basal-normalized mean log2 RNA/DNA activity for the alternate allele in ATRA replicate 3.
- atra_ref_activity_rep4
- Basal-normalized mean log2 RNA/DNA activity for the reference allele in ATRA replicate 4.
- atra_alt_activity_rep4
- Basal-normalized mean log2 RNA/DNA activity for the alternate allele in ATRA replicate 4.
- atra_ref_activity_rep5
- Basal-normalized mean log2 RNA/DNA activity for the reference allele in ATRA replicate 5.
- atra_alt_activity_rep5
- Basal-normalized mean log2 RNA/DNA activity for the alternate allele in ATRA replicate 5.
- atra_ref_activity_rep6
- Basal-normalized mean log2 RNA/DNA activity for the reference allele in ATRA replicate 6.
- atra_alt_activity_rep6
- Basal-normalized mean log2 RNA/DNA activity for the alternate allele in ATRA replicate 6.
- vehicle_ref_mean_activity_log2
- Mean available vehicle activity for the reference allele.
- vehicle_alt_mean_activity_log2
- Mean available vehicle activity for the alternate allele.
- vehicle_alt_minus_ref_log2fc
- Derived vehicle alternate-minus-reference difference in mean basal-normalized log2 activity.
- atra_ref_mean_activity_log2
- Mean available ATRA activity for the reference allele.
- atra_alt_mean_activity_log2
- Mean available ATRA activity for the alternate allele.
- atra_alt_minus_ref_log2fc
- Derived ATRA alternate-minus-reference difference in mean basal-normalized log2 activity.
- atra_minus_vehicle_effect_log2fc
- Derived change in allelic effect under ATRA relative to vehicle.
- published_mpra1_mean_log2fc
- Authors' published first-assay allelic mean log2 fold change, when present.
- published_vehicle_mean_log2fc
- Authors' published vehicle-condition allelic mean log2 fold change, when present.
- published_atra_mean_log2fc
- Authors' published ATRA-condition allelic mean log2 fold change, when present.
- published_first_assay_ttest_p
- Authors' published first-assay uncorrected allelic t-test p-value, when present.
- published_first_assay_empirical_q
- Authors' first-assay empirical q-value, when present.
- published_vehicle_ttest_p
- Authors' vehicle-condition t-test p-value, when present.
- published_vehicle_empirical_q
- Authors' vehicle-condition empirical q-value, when present.
- published_atra_ttest_p
- Authors' ATRA-condition t-test p-value, when present.
- published_atra_bh_fdr
- Authors' ATRA-condition Benjamini-Hochberg FDR, when present.
- published_lmm_allele_q
- Authors' empirical q-value for the LMM allele main effect, when present.
- published_lmm_drug_q
- Authors' empirical q-value for the LMM drug main effect, when present.
- published_lmm_interaction_q
- Authors' empirical q-value for the LMM allele-by-drug interaction, when present.
- published_lrt_interaction_vs_additive_p
- Authors' likelihood-ratio p-value comparing interaction and additive models, when present.
- published_first_assay_hit
- Authors' first-assay significance call (Yes/No), when present.
- published_first_and_vehicle_hit
- Authors' call for significance in both the first assay and vehicle condition, when present.
- published_second_assay_allele_effect
- Authors' second-assay allele main-effect call (Yes/No), when present.
- published_second_assay_interaction_effect
- Authors' second-assay allele-by-drug interaction call (Yes/No), when present.
- qc_pass
- TRUE for a row retained after the package QC filters.
Quality control
The authors' processed barcode-level expression tables were used after their DNA <75, RNA <30, minimum 4-barcode, minimum 3-replicate-observation, >2-standard-deviation outlier, and per-sample barcode-depth filters. Package-level eligibility additionally required analyze=YES, nonmissing expression values for both alleles, and no more than 60% missingness among the 240 expected barcode-by-condition values used by the LMM. The resulting table contains 1,181 of 1,454 candidate SNPs and only QC-passing rows. The article reports 1,079 SNPs for its LMM analysis; the discrepancy is documented because the deposited processed expression tables and the published count are not identical in their final missingness/analysis flags. Published single-condition statistics, LMM q-values, interaction calls, and LRT values are merged where available from the authors' 277-SNP summary.
Curation notes
The processed table is one row per eligible SNP and combines the authors' condition-specific post-QC barcode expression tables with the published summary statistics. Activity columns use the authors' basal-normalized element-level values; derived effects are explicitly alternate minus reference. The deposited tables retain 1,181 LMM-eligible SNPs under the stated 60%-missingness rule, whereas the manuscript reports 1,079 analyzed SNPs, so this provenance discrepancy is intentionally preserved rather than silently discarding otherwise usable deposited measurements.