These states—for example, neurotransmitter-driven programs in astrocytes or perivascular fibroblast differentiation—are obscured in eQTL studies that aggregate cells1,2. Here we modelled eQTLs at single-cell resolution in one complex cell type: memory T cells. Using more than 500,000 unstimulated ...
(2)任何表现出GWAS共定位和表达数量性状基因座(eQTL)信号的SNPs(FINEMAP/eCAVIAR共定位后验概率>0.01) (3)根据1000 Genomes数据集中欧洲血统个体的1期基因型计算的LD R2值≥0.8(有点绕:Any SNPs in LD with a SNP in the previous 2 categories based on an LD R2 value ≥0.8 calculated from phase 1 g...
1. Exploring the example dataset 在本次研讨会上,我们将使用单细胞RNA-seq数据集,该数据集是Kang等人(2017年)进行的一项较大研究的一部分。在本文中,作者提出了一种利用遗传变异(eQTL)来确定基因的计算算法。 每个包含单个细胞的液滴的遗传同一性(单一),并鉴定包含来自不同个体的两个细胞的液滴(双重)。 用于...
However, their performance has not been evaluated extensively in single-cell eQTL analysis, especially for different cell types. Potential challenges arise due to the structure of single-cell RNA-seq data, including sparsity, skewness, and mean-variance relationship. Here, we show by a series of ...
immune cells are overrepresented15. Given this complexity, even when bulk-tissue-based eQTL identified multiple candidate target genes, it is difficult to determine in which cell types (e.g., cells of cancer origin vs. immune cells) the lung cancer susceptibility genes might be functional. More...
At 1% BH FDR and log2FC > 0.25 for the bulk RNA-seq data in adult transverse colon data, we compared these upregulated genes with the top genes in scRNA-seq and the top genes in expression quantitative trait loci (eQTL) (eGenes) and splicing QTL (sQTL) (sGenes) of WGS of th...
Single-cell eQTL models reveal dynamic T cell state dependence of disease loci Nucleic Acids Res 16.971 Single-cell genome-wide concurrent haplotyping and copy-number profiling through genotyping-by-sequencing Blood 23.629 Single-cell multiomics reveal the scale of multi-layered adaptations enabling CLL...
Single nucleotide polymorphism (SNP), a common form of genetic variation, is caused by the transition, transversion, insertion, or deletion of individual bases. Expression quantitative trait loci (eQTL) analysis can profile genetic variations (especially SNP) that affect gene expression, offering enhan...
optimising_singlecell_eqtl_paperPublic Repository containing the code to reproduce the analyses contained in our manuscript: Optimising expression quantitative trait locus mapping workflows for single-cell studies Jupyter Notebook5Apache-2.0100UpdatedJun 28, 2024 ...
The majority (86.1–91.8%) of sc-eGenes has only one sc-eQTL set per cell type (Additional file 1: Fig. S2b). Interestingly, most of sc-eQTLs are cell type-specific, with 87.0–92.3% identified in only one cell type (Fig. 2a). Furthermore, the remaining sc-eQTLs that are observed...