Adult female Vglut1-positive hippocampal TRAP MPRA validation cohort
Sex significantly impacts the function of major depression-linked variants in vivoThree additional adult female samples from a pilot of the hippocampal Vglut1-TRAP MPRA were used as a validation cohort. This table preserves the published allelic betaA2 and empirical-p-derived q summaries for Vglut1-positive glutamatergic hippocampal neuron RNA.
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
This is the additional n=3 adult female validation cohort from the same AAV9 hsp68 minimal-promoter reporter library. Vglut1-positive hippocampal RNA was obtained by TRAP and compared with the main adult female Vglut1-TRAP experiment using published betaA2 and empirical-p-derived q values.
Processed data
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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 · 15 definitions
- rsid
- dbSNP identifier for the tested SNP.
- snp_hg19_coordinate
- SNP coordinate on the hg19 reference assembly, joined from the adult library result table.
- reference_allele
- A1 allele used as the reference in the source LMM.
- effect_allele
- A2 allele whose betaA2 is reported relative to A1.
- annotation_sources
- MDD/locus or other source labels from the authors' library annotation.
- ldblock_id
- LD block or locus identifier from the authors' library annotation.
- maf
- Minor-allele frequency in the authors' library annotation; population is not re-inferred here.
- ld_r2
- Source annotation R-squared value for the SNP/tag relationship.
- tag_snp
- Tag SNP listed in the source library annotation.
- library_reference_allele
- Reference allele in the source library annotation.
- library_alternate_allele
- Alternate allele in the source library annotation.
- main_q_empirical_p
- Empirical-p q value for the main adult female Vglut1-TRAP analysis.
- main_betaA2
- Main adult female Vglut1-TRAP betaA2, with A2 relative to A1.
- replication_q_empirical_p
- Empirical-p q value for the additional female Vglut1-TRAP validation cohort.
- replication_betaA2
- betaA2 for the additional female Vglut1-TRAP validation cohort, with A2 relative to A1.
Quality control
The authors describe the validation cohort as undergoing the same MPRA sequencing analysis and barcode QC as the main adult experiments; all samples used for sequencing preparation had RNA integrity number >=6. The analysis used DNA/RNA barcode-count thresholds, at least 4 barcodes per element/sample, representation in at least 50% of samples, removal of >=2 standard-deviation barcode outliers, hsp68 minimal-promoter normalization, barcode-random-effect mixed models, and 50,000 empirical null comparisons. Package QC retained rows with at least one published betaA2 or empirical-p q value and a valid library coordinate and allele pair; blank values mean that the corresponding summary was not reported or did not pass source filtering.
Curation notes
Data were extracted from Data_S1, which reports empirical-p q values and allelic log2 fold-change/betaA2 for the main adult female experiment (n=5) and the additional validation cohort (n=3). The validation cohort's total hippocampal RNA is packaged separately as E1A491475. Data_S1 does not provide standard errors or uncorrected p values. One retained SNP (rs77910749) has no matching row in the archived library annotation file and therefore has blank annotation fields.