Mouse brain MPRA — hippocampus
Context-dependent regulatory variants in Alzheimer’s diseaseVariant-focused in vivo AAV-MPRA profiling of the paired alternative/reference library in mouse hippocampus. Adult mice received the barcoded reporter library by AAV-PHP.eB delivery and tissue was collected four weeks after the second injection.
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
AAV-PHP.eB library delivery; no exogenous treatment; tissue collected 4 weeks after the second retro-orbital injection
AAV-PHP.eB packaged the synthetic barcoded MPRA library for systemic delivery to adult C57BL/6J mice; hippocampal reporter activity was measured as tissue cDNA/DNA ratios with MPRAnalyze.
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 · 54 definitions
- construct_id
- Alternative-allele MPRA construct identifier from the study design.
- reference_construct_id
- Reference/background construct paired to construct_id in the study’s MPRA_REF_ALT mapping.
- variant_id
- Variant identifier (usually dbSNP rsID; includes cg IDs for methylation-array-derived candidates).
- chromosome
- GRCh38 chromosome number for the tested construct.
- position_hg38
- GRCh38 position of the indexed candidate variant, taken from the study’s construct-aligned snp(hg19+hg38) field; raw source fields are preserved in media-3.xlsx.
- reference_allele
- Reference allele recorded in the study design.
- alternate_allele
- Alternate allele represented by construct_id.
- major_allele
- Allele designated Major by the study’s population annotation.
- minor_allele
- Allele designated Minor by the study’s population annotation.
- refalt_flip
- Study flag indicating whether the reported reference/alternate orientation is flipped relative to Major/Minor.
- construct_center_type
- Whether the construct was centered on a SNP or a regulatory peak.
- peak_start_hg38
- Start of the broad GRCh38 MPRA construct interval.
- peak_end_hg38
- End of the broad GRCh38 MPRA construct interval.
- peak_summit_hg38
- GRCh38 center/summit used for the construct.
- closest_protein_coding_gene
- Closest protein-coding gene to the tested locus according to the study annotation.
- distance_to_closest_protein_coding_tss
- Distance in base pairs to the closest protein-coding transcription start site.
- regulatory_annotation
- Hierarchical regulatory annotation from the study.
- rsid_gene_tss_annotation
- Study’s variant-to-gene/TSS annotation label.
- cre_annotation
- Candidate cis-regulatory-element annotation.
- rare_common
- Study classification of the candidate as Rare or Common.
- gc_content
- GC content value reported for the tested sequence (the supplement expresses this as a percentage-like value).
- gwas_bellenguez_p_value
- Bellenguez et al. GWAS p-value recorded by the study.
- gwas_bellenguez_neg_log10_p
- Negative log10 of the Bellenguez et al. GWAS p-value.
- motif_mef2
- Study motif annotation for MEF2.
- motif_pu1
- Study motif annotation for PU.1.
- motif_irf
- Study motif annotation for IRF.
- motif_stat
- Study motif annotation for STAT.
- motif_nf_kappa_b
- Study motif annotation for NF-κB.
- motif_ap1
- Study motif annotation for AP-1.
- allelic_log2fc_major_vs_minor
- MPRAnalyze allelic effect normalized to Major minus Minor log2 reporter activity.
- allelic_statistic
- MPRAnalyze test statistic for the allelic comparison.
- allelic_p_value
- Unadjusted MPRAnalyze p-value for the allelic comparison.
- allelic_fdr
- FDR-adjusted MPRAnalyze p-value for the allelic comparison.
- allelic_df_test
- Degrees of freedom for the allelic test.
- allelic_df_dna
- DNA-model degrees of freedom for the allelic test.
- allelic_df_rna_full
- Full RNA-model degrees of freedom for the allelic test.
- allelic_df_rna_reduced
- Reduced RNA-model degrees of freedom for the allelic test.
- major_activity_mad_score
- MPRAnalyze MAD activity score for the Major-allele construct.
- minor_activity_mad_score
- MPRAnalyze MAD activity score for the Minor-allele construct.
- major_activity_p_mad
- MPRAnalyze MAD activity p-value for the Major-allele construct.
- minor_activity_p_mad
- MPRAnalyze MAD activity p-value for the Minor-allele construct.
- major_activity_z_score
- MPRAnalyze z-score for the Major-allele construct.
- minor_activity_z_score
- MPRAnalyze z-score for the Minor-allele construct.
- major_activity_p_zscore
- MPRAnalyze z-score p-value for the Major-allele construct.
- minor_activity_p_zscore
- MPRAnalyze z-score p-value for the Minor-allele construct.
- enhancer_activity_qc
- TRUE when either allele has study-defined active-enhancer pval.mad < 0.05; FALSE otherwise.
- emvar_qc
- TRUE when the study-defined allelic FDR is < 0.05; FALSE otherwise.
- stimulus_vs_resting_log2fc
- Construct-level activity log2 fold-change versus the matched resting state, when reported.
- stimulus_vs_resting_p_value
- Unadjusted p-value for construct activity change versus the matched resting state, when reported.
- stimulus_vs_resting_fdr
- FDR for construct activity change versus the matched resting state, when reported.
- ml_predicted_log2fc_model_1
- Study-reported interpretable ML predicted chromatin log2 fold-change for model 1; blank where no exact context model was supplied.
- ml_predicted_log2fc_model_2
- Study-reported interpretable ML predicted chromatin log2 fold-change for model 2; blank where no exact context model was supplied.
- ml_prediction_model_1
- Name of the ML prediction column used for model 1.
- ml_prediction_model_2
- Name of the ML prediction column used for model 2.
Quality control
The study excluded 21 enhancers with underrepresented genomic-DNA barcode counts and used 15 barcode replicates for the standard analyses; its sparse brain and THP-1 monocyte datasets were handled with five pseudo-barcodes formed by summing groups of three. For this package, only non-empty alternative constructs with an exact design record, an explicit alt-to-reference mapping, matching activity rows for both paired constructs, and numeric MPRAnalyze allelic statistics were retained. The enhancer_activity_qc and emvar_qc columns expose the study thresholds (pval.mad < 0.05 and FDR < 0.05) without removing biologically inactive or non-significant tested variants.
Curation notes
For some constructs, the supplement’s pos_hg38/coordinate fields disagree with the construct-aligned snp(hg19+hg38) value and encoded construct interval; position_hg38 in this processed table follows the latter so it matches the assayed sequence, while the raw workbook preserves the original fields. The reporter sequences and variant coordinates are human GRCh38 constructs assayed in mouse tissue. The manuscript’s ML supplement has no hippocampus-specific prediction column, so those fields are blank.