Adult female hippocampal total-RNA 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 q summaries for total hippocampus, including separate 66-ng and 150-ng technical input analyses and their joint 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
Basal / Untreated
This is the additional n=3 adult female validation cohort from the same AAV9 hsp68 minimal-promoter reporter library. Total hippocampal RNA was prepared for sequencing at 66 ng and 150 ng input per sample; the source analyzed these technical input sets separately and jointly and reported betaA2 and empirical-p-derived q values.
Processed data
50 rows per page. Click a cell to inspect its full value.
Visible columns (19 of 19)
| 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 · 19 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 total-hippocampus analysis.
- main_betaA2
- Main adult female total-hippocampus betaA2, with A2 relative to A1.
- replication_hippocampus_66ng_q_empirical_p
- Empirical-p q value for the validation cohort's 66-ng total-hippocampus RNA input analysis.
- replication_hippocampus_66ng_betaA2
- betaA2 for the validation cohort's 66-ng total-hippocampus RNA input analysis.
- replication_hippocampus_150ng_q_empirical_p
- Empirical-p q value for the validation cohort's 150-ng total-hippocampus RNA input analysis.
- replication_hippocampus_150ng_betaA2
- betaA2 for the validation cohort's 150-ng total-hippocampus RNA input analysis.
- replication_hippocampus_joint_q_empirical_p
- Empirical-p q value for the joint analysis of the 66-ng and 150-ng validation input sets.
- replication_hippocampus_joint_betaA2
- betaA2 for the joint analysis of the 66-ng and 150-ng validation input sets.
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 Vglut1-positive fraction is packaged separately as E07789719; the 66-ng and 150-ng labels refer to technical input RNA amounts for total hippocampus, not separate biological treatments. 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.