Experiment / E4796B137AAV-MPRA / in vivo MPRA

Adult mouse Vglut1-positive hippocampal TRAP 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 Vglut1-TRAP mice. Anti-eGFP TRAP RNA from Vglut1-positive glutamatergic hippocampal neurons 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: CL:0000679
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; bilateral adult hippocampal delivery was followed by translating ribosome affinity purification of the Vglut1-positive 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 Vglut1-TRAP 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 Vglut1-TRAP 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 D (male), E (female), G (SxG), and P/Q (sex-specific beta estimates). The RNA fraction is translating-ribosome-affinity-purified Vglut1-positive glutamatergic hippocampal neuron RNA from the adult bilateral hippocampal AAV9 cohort; CL:0000679 describes the cell type, while the tissue context is recorded in this description. The source SxG output provides interaction p/q values and flags plus a combined-sex allele beta, but no separate interaction beta coefficient. One retained SNP (rs77910749) has no matching row in the archived library annotation file and therefore has blank annotation fields.

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