Experiment / E7EF7B69EAAV-MPRA / in vivo MPRA

Adult mouse total hippocampus AAV9 variant MPRA

Sex significantly impacts the function of major depression-linked variants in vivo

An AAV9 MPRA library of allelic 126-bp human hg19 sequence inserts was delivered bilaterally to the hippocampus of adult mice. Reporter RNA from total/input hippocampus was compared with AAV DNA in male and female animals to estimate allele effects and sex-by-allele interactions.

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Organism: Mouse
Taxonomy ID: NCBITaxon:10090
Biosample: UBERON:0002421
Reference genome: hg19
Design focus: Variant-focused
Region of interest: Not reported / not applicable

Perturbation & assay details

Basal / Untreated

AAV9-packaged hsp68 minimal-promoter reporter constructs carried allele-specific 126-bp human hg19 SNP-centered inserts, with approximately 10 unique 10-bp barcodes per allele. Inserts were cloned upstream of dsRed and a woodchuck hepatitis virus 3-prime UTR element for reporter-RNA recovery; the processed output is the total/input hippocampal RNA fraction.

Processed data

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Column dictionary · 52 definitions

rsid: dbSNP identifier for the tested SNP.
snp_hg19_coordinate: SNP coordinate on the hg19 reference assembly.
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.
male_betaA2: Male total-hippocampus LMM beta for A2 relative to A1.
male_SE_betaA2: Standard error of male betaA2.
male_lmm_p: Male default LMM p value for the allele effect.
male_empirical_p: Male empirical p value for the allele effect.
male_q_lmm_p: Male q value after correction of the default LMM p values.
male_q_empirical_p: Male q value after correction of empirical p values.
male_significant_lmm_fdr_0_05: Source boolean flag for default-LMM q <0.05.
male_significant_empirical_fdr_0_05: Source boolean flag for empirical q <0.05.
male_significant_empirical_fdr_0_10: Source boolean flag for empirical q <0.10.
male_significant_empirical_fdr_0_15: Source boolean flag for empirical q <0.15.
male_significant_empirical_fdr_0_20: Source boolean flag for empirical q <0.20.
male_significant_empirical_fdr_0_25: Source boolean flag for empirical q <0.25.
female_betaA2: Female total-hippocampus LMM beta for A2 relative to A1.
female_SE_betaA2: Standard error of female betaA2.
female_lmm_p: Female default LMM p value for the allele effect.
female_empirical_p: Female empirical p value for the allele effect.
female_q_lmm_p: Female q value after correction of the default LMM p values.
female_q_empirical_p: Female q value after correction of empirical p values.
female_significant_lmm_fdr_0_05: Source boolean flag for default-LMM q <0.05.
female_significant_empirical_fdr_0_05: Source boolean flag for empirical q <0.05.
female_significant_empirical_fdr_0_10: Source boolean flag for empirical q <0.10.
female_significant_empirical_fdr_0_15: Source boolean flag for empirical q <0.15.
female_significant_empirical_fdr_0_20: Source boolean flag for empirical q <0.20.
female_significant_empirical_fdr_0_25: Source boolean flag for empirical q <0.25.
sxg_allele_lmm_p: Combined-sex LMM p value for the allele main effect in the SxG model.
sxg_sex_lmm_p: Combined-sex LMM p value for the sex main effect in the SxG model.
sxg_lmm_p_interaction: LMM p value for the sex-by-allele interaction.
sxg_allele_empirical_p: Combined-sex empirical p value for the allele main effect in the SxG model.
sxg_sex_empirical_p: Combined-sex empirical p value for the sex main effect in the SxG model.
sxg_empirical_p_interaction: Empirical p value for the sex-by-allele interaction.
sxg_q_lmm_p_interaction: FDR-adjusted q value for the SxG LMM p value.
sxg_q_empirical_p_interaction: FDR-adjusted q value for the SxG empirical p value.
sxg_significant_lmm_fdr_0_05: Source boolean flag for SxG default-LMM q <0.05.
sxg_significant_empirical_fdr_0_05: Source boolean flag for SxG empirical q <0.05.
sxg_significant_empirical_fdr_0_10: Source boolean flag for SxG empirical q <0.10.
sxg_significant_empirical_fdr_0_15: Source boolean flag for SxG empirical q <0.15.
sxg_significant_empirical_fdr_0_20: Source boolean flag for SxG empirical q <0.20.
sxg_significant_empirical_fdr_0_25: Source boolean flag for SxG empirical q <0.25.
combined_sex_allele_betaA2: Combined-sex allele-main-effect betaA2 reported in the SxG model.
combined_sex_allele_SE_betaA2: Standard error of the combined-sex allele-main-effect betaA2.
combined_sex_allele_q_empirical_p: Empirical-p q value for the combined-sex allele main effect.

Quality control

Authors retained 5 adult samples per sex and RNA fraction after quality control from n=6 per sex. Barcode QC required DNA count >=187 (or the approximate CPM equivalent), RNA count >=75, at least 4 retained barcodes per regulatory element/sample, barcode representation in at least 50% of samples, and removal of individual barcode/sample outliers >=2 standard deviations; expression was normalized to the mean hsp68 minimal-promoter barcode activity. Linear mixed models used barcode as a random effect and 50,000 simulated minimal-promoter barcode comparisons for empirical p values; the source's principal rSNP threshold was empirical q <0.20. Package QC additionally removed rows with no finite published model result and required a valid coordinate and A1/A2 allele pair.

Curation notes

Rows were joined from Data_S2 sheets B (male), C (female), F (SxG), and N/O (sex-specific beta estimates). The adult total/input hippocampus fraction came from the bilateral adult hippocampal AAV9 cohort. The source SxG output provides interaction p/q values and flags plus a combined-sex allele beta, but no separate interaction beta coefficient; blank cells indicate source values not estimable or not present after source filtering. One retained SNP (rs77910749) has no matching row in the archived library annotation file and therefore has blank annotation fields.

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