SingleBrain: Single-nucleus Trans Expression QTL Meta-analysis Summary Statistics across Multiple Human Brain Cohorts

https://github.com/RajLabMSSM/SingleBrain Bonferroni significant association summary statistics for trans-eQTLs mapped in a meta-analysis across multiple human brain single-nucleus RNA seq cohorts, as part of the "SingleBrain" project. Sample size = 983 European ancestry donors from 757 unique donors 4 cohorts (Fujita et al., Mathys et al., Bryois et al., Gabitto et al.) meta-analyzed using the linear mixed model random-effects meta-analysis software mmQTL (PMID: 35058635). Number of tested SNPs = 265,814 Bonferroni threshold = 0.05/(#genesTested x #variantsTested) Each file has the following naming convention: {Cell type}_trans_eqtl_peak_1_sig_assoc.tsv.gz References The following reference was used for mapping phenotypes: 1. GENCODE - GENCODE v38 comprehensive transcripts (https://www.gencodegenes.org/human/release_38.html) Cell type The following brain 6 major cell types were tested for genetic association: Ast: astrocytes Ext: excitatory neurons IN: inhibitory neurons MG: microglia OD: oligodendrocytes OPC: oligodendrocyte progenitor cell All phenotype matrices were scaled and centered and then quantile normalized. Data dictionary feature: the phenotype being tested variant_id: the genetic variant being tested chr: chromosome pos: position (hg38) ref: reference allele alt: alternate allele fixed_beta: Fixed effect meta-analysis estimate of the beta fixed_sd: Fixed effect meta-analysis standard error of the beta fixed_z: Fixed effect meta-analysis Z-score Fixed_P: Fixed effect meta-analysis P-value Random_Z: Random effect meta-analysis Z-score Random_P: Random effect meta-analysis P-value cis_feature: cross-mappable gene pair with feature crossmap: cross-mappable gene pairs estimated using Saha et al.[PMID: 30613398] are filtered less than 5.https://github.com/RajLabMSSM/SingleBrain 本数据集为"SingleBrain"项目的组成部分，包含跨多个人类大脑单细胞核RNA测序队列开展荟萃分析后定位的反式表达数量性状基因座（trans-eQTL）的邦费罗尼显著性关联汇总统计量。 样本量：983份样本源自757名独立的欧洲血统供体。 本研究对4个队列（Fujita等、Mathys等、Bryois等、Gabitto等）的数据采用线性混合模型随机效应荟萃分析软件mmQTL（PMID: 35058635）完成荟萃分析。 本次测试的单核苷酸多态性（SNP）总数为265,814。 邦费罗尼校正阈值为0.05/(检测基因数 × 检测变异数)。 所有文件均遵循如下命名格式： {细胞类型}_trans_eqtl_peak_1_sig_assoc.tsv.gz ### 参考文献 本研究用于表型定位的参考文献如下： 1. GENCODE：GENCODE v38综合转录本（https://www.gencodegenes.org/human/release_38.html） ### 细胞类型 本次测试了以下6种主要大脑细胞类型的遗传关联： - Ast：星形胶质细胞（Astrocytes） - Ext：兴奋性神经元（Excitatory neurons） - IN：抑制性神经元（Inhibitory neurons） - MG：小胶质细胞（Microglia） - OD：少突胶质细胞（Oligodendrocytes） - OPC：少突胶质细胞前体细胞（Oligodendrocyte progenitor cell） 所有表型矩阵均经标准化、中心化处理后，再进行分位数归一化。 ### 数据字典 各字段说明如下： - feature：待测试的表型 - variant_id：待测试的遗传变异标识符 - chr：染色体 - pos：基因组位置（hg38版本） - ref：参考等位基因 - alt：替代等位基因 - fixed_beta：β值的固定效应荟萃分析估计值 - fixed_sd：β值的固定效应荟萃分析标准误 - fixed_z：固定效应荟萃分析Z得分 - Fixed_P：固定效应荟萃分析P值 - Random_Z：随机效应荟萃分析Z得分 - Random_P：随机效应荟萃分析P值 - cis_feature：与待测试表型存在交叉映射的基因对 - crossmap：采用Saha等人[PMID: 30613398]的方法估算得到的交叉映射基因对，已过滤掉交叉映射评分小于5的结果。