RNA profiling data of IL13Ra2 CAR-T cells

Description

This study was designed to evaluate differences in gene expression in between different CAR-T cell constructs directed against interleukin 13 receptor alpha-2 (IL13Rα2). CAR-T cells were isolated by flow sorting and subjected to targeted bulk-RNA profiling using Nanostring nCounter CAR-T Characterization panel followed by downstream analysis. Data consists of the CAR[B]-, CAR[E]- and Mock-T cell constructs generated from 4 healthy donors. 1. 12 individual RCC files contanig the raw gene expression data for the 3 constructs x 4 donors 2. rlf annotation file 3. QC and Normalized data as a txt file

Steps to reproduce

Gene expression count matrices went through an internal QC process, and were normalized with a set of automatically refined housekeeping genes determined using the default nCounter advanced analysis module with the nSolver4.0 software (NanoString Technologies). Differential gene expression between CAR constructs and the top 20 active signaling pathways was performed using the Fast/Approximate negative binomial model, the adjusted p-values were calculated using Benjamini-Yekutieli method (FDR p<0.05) in nSolver4.0. In addition normalized gene expression data from nSolver were also imported to Partek Flow gene expression analysis software (Partek Inc.) for further analysis (Partek flow 10.0.22.0828). To determine the differentially expressed genes (DEG) the data was first normalized using TMM method and differentially expressed genes were then determined using DESeq2. Genes with fold change less than -1.49 or more than 1.49 and FDR p<0.05 were selected to make a heatmap of the DEG between CAR[B]-T vs CAR[E]-T + Mock-T cells.

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