Mapping expression quantitative trait loci (eQTL) provides insight into gene expression regulation. When RNA-Seq data is used to fit eQTL, proper statistical analysis requires addressing issues such as: (1) Shrinking variance component estimates to increase power of eQTL detection in small samples, ...
Second, it generates unprecedentedly rich data to study RNA-isoform expression. In this paper, we review current methods for eQTL mapping using ASE and discuss some future directions. We also review existing works that use RNA-seq data to study RNA-isoform expression and we discuss the gaps ...
Separating measurement and expression models clarifies confusion in single-cell RNA sequencing analysis. Nat. Genet. 53, 770–777 (2021). Article CAS PubMed PubMed Central Google Scholar Hafemeister, C. & Satija, R. Normalization and variance stabilization of single-cell RNA-seq data using ...
1, Supplementary Data 1, Supplementary Data 2). We characterized the fetal-like pancreatic transcriptome as well as the cellular composition using single-cell RNA-seq (scRNA-seq) of eight iPSC-PPC samples. Then, we conducted an eQTL analysis on bulk RNA-seq of all 107 samples to identify ...
This study is the first to use expression quantitative trait loci (eQTL) mapping of transcript-derived markers for TSC in potato. Thirty-four differentially expressed genes were selected by comparing the RNA-seq data of contrasting bulked segregants. For the 11 candidate genes, we determined their...
For each gene, expression values were transformed using the Box-Cox method [103] prior to mapping 西红柿泛基因组 eQTL分析部分方法 Genes with TPM values of >0.5 were defined as expressed. Only genes expressed in at least 100 accessions were retained for the downstream analyses. Raw expression le...
RNA-Sequencing (RNA-Seq) experiments have been optimized for library preparation, mapping, and gene expression estimation. These methods, however, have revealed weaknesses in the next stages of analysis of differential expression, with results sensitive to systematic sample stratification or, in more ex...
In this study, we first ran a comprehensive GWAS analysis for 21 agronomic traits using imputed whole-genome variants in Simmental beef cattle. We then applied eQTL mapping in three tissues (longissimus dorsi muscle, backfat, and liver) using 356 samples from 120 cattle (Fig. 1a and Fig. ...
Finally, we evaluated whether the signature genes showed CT expression in their rele- vant purified cell types using BLUEPRINT [23] RNA-seq data from the purified cell subpopulations. Here we focused on cell types with more than three samples measured, which included neutrophils, CD14+ monocytes...
params{method= 'single_cell' //or a [bulk | single_cell] (if single cell used the *phenotype_file* is a h5ad file)input_vcf ='/path/to/genotype/vcf/file.vcf'genotype_phenotype_mapping_file = '' //if bulk RNA seq data is fed in then need a tsv file with 3 columns - [Genotyp...