et al. Cell-type-specific cis-eQTLs in eight human brain cell types identify novel risk genes for psychiatric and neurological disorders. Nat. Neurosci. 25, 1104–1112 (2022). This study is one of the only single-cell eQTL studies in tissue to date. Article CAS PubMed Google Scholar ...
as it analyzes much larger sample sizes than single-tissue and multi-tissue methods that rely on individual-level data. When compared to PUMICE, PrediXcan, FUSION, TIGAR, EpiXcan, DePMA and MeTWAS trained on GTEx whole blood tissue, EXPRESSO-PVS trained on ...
one cell type from AIDA, colored as ina.g, Fractions of leadcis-sQTLs shared according to sign and magnitude in one or more cell types. Sharing according to sign was defined as acis-sQTL sharing the same sign with the topcis-sQTL across 19 cell types. Sharing according to magnitude was...
Genome-wide association studies have identified over 200 loci associated with CAD, where the majority of risk variants reside in noncoding DNA sequences impacting cis-regulatory elements. Here, we applied single-nucleus assay for transposase-accessible chromatin with sequencing to profile 28,316 nuclei...
rs1582763 is also a cis〆QTL for both MS4A4A and MS4A6A genes in bulk RNA﹕eq of blood. We generated unsorted single‐nuclei RNA﹕eq from human brain tissue from the Knight〢DRC brain bank. We collected the parietal lobe for 30 AD brains (19 are carriers of the rs1582763 minor ...
capturing and understanding these genetic effects is an enormous challenge. Resolving these effects to specific cell types using classical quantitative trait loci (QTL) mapping would require FACS sorting different cell types from a heterogeneous tissue across a large panel of individuals, a huge task ...
In our database, we found a cis-eQTL for TRPM1 in RPE/choroid tissue, but not in the retina (Figures 6A and 6B). TRPM1 is regulated in cis on the basis of allele-specific expression, which is based on data from coding SNPs in TRPM1 (Figure 6C). Co-localization of the genetic ...
We propose SCALE, a statistical framework to study ASE using scRNA-seq data. The input data to SCALE are allele-specific read counts at heterozygous loci across all cells. In the two datasets that we analyzed, we used F1 mouse crossing and bulk-tissue sequencing to profile the true heterozygo...
deemed appropriate for single-cell sequencing, whereas freeze-thaw samples are generally recommended for snRNA-seq [242,243]. Besides, the quantity and viability of the cell suspension are also important factors in obtaining high-quality single-cell data and detecting all cell types in the tissue....
2.3 eQTL and mQTL data source The eQTLGen consortium (https://www.eqtlgen.org/cis-eqtls.html) provided the whole blood eQTL dataset, which included 31,684 individuals [35]. The eQTL dataset of specific lung tissue was obtained from the GTEx database (https://gtexportal.org/home/), which...