referenced paper: Generation and function of progenitor T cells from StemRegenin-1–expanded CD34+ human hematopoietic progenitor cells
PMID: 31648315
GSEID: GSE135927
Dataset description:gene expression profile of single cell peripheral CD3+ cells from immunodeficient mice injected with human progenitor T-cells (proT-cells). ProT-cell subsets were generated in vitro using human umbilical cord blood-derived CD34+ cells that were either non-expanded (naive), or expanded in vitro with the hydrocarbon receptor antagonist, StemRegenin-1 (SR1)
.
Purpose of this project: Learn how to collect public available data from Gene Expression Omnibus database. Introduction to single cell rna-seq bioinformatics analysis and package “seurat”.
Experimental design:
• Quality control on scRNAseq data
• Normalize scRNAseq data
• Feature selection to identify highly variable features
o Help highlight biological signals in single cell dataset
• Normalize data for pca analysis
• PCA
o Determine optimal dimensionality of dataset
• tSNE non-linear dimensional reduction
o to place similar cells together in low-dimensional space.
• Find cluster biomarkers that define each cluster
o Assigning cell type identity to clusters
References:
Andrews TS, Kiselev VY, McCarthy D, Hemberg M. Tutorial: guidelines for the computational analysis of single-cell RNA sequencing data. Nature protocols. 2021 Jan;16(1):1-9.
Singh J, Chen EL, Xing Y, Stefanski HE, Blazar BR, Zúñiga-Pflücker JC. Generation and function of progenitor T cells from StemRegenin-1–expanded CD34+ human hematopoietic progenitor cells. Blood advances. 2019 Oct 22;3(20):2934-48.
Hao Y, Hao S, Andersen-Nissen E, Mauck III WM, Zheng S, Butler A, Lee MJ, Wilk AJ, Darby C, Zager M, Hoffman P. Integrated analysis of multimodal single-cell data. Cell. 2021 May 31.
