Baseline plasmid MPRA of psychiatric risk SNPs in Neuro-2a cells
Transcriptional-regulatory convergence across functional MDD risk variants identified by massively parallel reporter assaysA pooled library of human hg19 SNP-centered allele tiles was transfected into mouse Neuro-2a cells without drug treatment. Each allele was represented by up to ten unique 10-bp barcodes, and reporter RNA activity was quantified relative to delivered plasmid DNA across six replicate wells.
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
Episomal plasmid MPRA using human hg19 allele tiles up to 126 bp centered on each candidate SNP, ten unique 10-bp barcodes per allele, an hsp68 minimal promoter driving dsRed, and a WPRE RNA-stabilization element. The pooled plasmid was delivered by Lipofectamine 2000; targeted reporter-barcode RNA and input-plasmid DNA were sequenced, and activity was calculated from log2 RNA/DNA barcode expression with basal-barcode normalization. Six wells were assayed, with three at each of two initial plating densities.
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 · 41 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_dna_barcodes_after_qc
- Number of reference-allele barcode oligos remaining after DNA and replicate QC.
- alt_dna_barcodes_after_qc
- Number of alternate-allele barcode oligos remaining after DNA and replicate QC.
- ref_barcode_n_after_qc
- Number of reference barcodes contributing at least one post-QC expression value.
- alt_barcode_n_after_qc
- Number of alternate barcodes contributing at least one post-QC expression value.
- ref_valid_replicates
- Number of replicate-level reference activity means available after QC.
- alt_valid_replicates
- Number of replicate-level alternate activity means available after QC.
- ref_activity_rep1
- Basal-normalized mean log2 RNA/DNA activity for the reference allele in replicate 1 (HD1).
- ref_activity_rep2
- Basal-normalized mean log2 RNA/DNA activity for the reference allele in replicate 2 (HD2).
- ref_activity_rep3
- Basal-normalized mean log2 RNA/DNA activity for the reference allele in replicate 3 (HD3).
- ref_activity_rep4
- Basal-normalized mean log2 RNA/DNA activity for the reference allele in replicate 4 (MH1).
- ref_activity_rep5
- Basal-normalized mean log2 RNA/DNA activity for the reference allele in replicate 5 (MH2).
- ref_activity_rep6
- Basal-normalized mean log2 RNA/DNA activity for the reference allele in replicate 6 (MH3).
- alt_activity_rep1
- Basal-normalized mean log2 RNA/DNA activity for the alternate allele in replicate 1 (HD1).
- alt_activity_rep2
- Basal-normalized mean log2 RNA/DNA activity for the alternate allele in replicate 2 (HD2).
- alt_activity_rep3
- Basal-normalized mean log2 RNA/DNA activity for the alternate allele in replicate 3 (HD3).
- alt_activity_rep4
- Basal-normalized mean log2 RNA/DNA activity for the alternate allele in replicate 4 (MH1).
- alt_activity_rep5
- Basal-normalized mean log2 RNA/DNA activity for the alternate allele in replicate 5 (MH2).
- alt_activity_rep6
- Basal-normalized mean log2 RNA/DNA activity for the alternate allele in replicate 6 (MH3).
- ref_mean_activity_log2
- Mean of available reference-allele replicate activity values.
- alt_mean_activity_log2
- Mean of available alternate-allele replicate activity values.
- alt_minus_ref_log2fc
- Derived alternate-minus-reference difference in mean basal-normalized log2 activity.
- qc_missing_allele_replicate_means
- Number of missing allele-by-replicate activity means among the 12 expected values.
- published_mpra1_mean_log2fc
- Authors' published first-assay allelic mean log2 fold change, when present in the summary table.
- published_first_assay_ttest_p
- Authors' published uncorrected first-assay allelic t-test p-value, when present.
- published_first_assay_empirical_q
- Authors' empirical q-value for the first-assay allelic test, 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 second-assay vehicle condition, when present.
- qc_pass
- TRUE for a row retained after the package QC filters.
Quality control
GEO unfiltered barcode counts were reprocessed using the authors' stated thresholds: DNA barcodes with <75 counts were removed; allele sequences with <4 DNA-supported barcodes were removed; RNA barcode counts <30 per sample were removed; barcode expression outliers >2 standard deviations from the allele mean within a sample were removed; barcodes observed in <3 of 6 RNA replicates were removed; allele/sample groups with <4 remaining barcodes were removed; and SNPs lacking at least two valid allele-level replicate means for either allele were excluded. The resulting table contains 1,011 of 1,454 candidate SNPs and only QC-passing rows. The article reports 1,013 analyzed SNPs; the two-row difference is noted as a deposited-count/version or boundary-handling discrepancy. Published first-assay statistics and hit calls are merged where available from the authors' 277-SNP summary.
Curation notes
The processed table is one row per QC-passing SNP and reports allele-level activity in six untreated Neuro-2a replicates. Effects are explicitly calculated as alternate minus reference; source summary statistics are retained separately because the authors used empirical basal-barcode calibration rather than a conventional FDR for this assay. The two-density design was reported as having no detectable density effect. The library includes a CDKAL1 negative-control locus and a positive control sequence, but these non-SNP controls are not represented in table.csv because the table is variant-focused.