Fiumara_BasePrimeEd2022_RNAseq

Fiumara M, Ferrari F, Omer-Javed A, Beretta S et al. Discovery and mitigation of genotoxic effects of base and prime editing in human hematopoietic stem cells. Nature Biotechnology 2023.

• RNA-seq Base Editing: GSE218462
• RNA-seq Prime Editing: GSE218463

Analyses

RNA-seq analysis to compare Treated (BE4, ABE8, Cas9, Mock electro) vs Untreated samples at Day1 or Day3 (GSE218462), and Prime edited vs Mock electro samples (GSE218463):

• input pre-processing with FastQC and quality trimming with Trimmomatic;
• read alignments to the human genome assembly (GRCh38) with the STAR using standard parameters;
• gene quantification computed with featureCounts;
• Differential Gene Expression (DGE) analysis with the R/Bioconductor package DESeq2: genes having FDR < 0.05 were considered as differentially expressed
• post-analyses with the R/Bioconductor package ClusterProfiler using the Hallmark collection from MSigDB as reference database.
• visualization of the (spliced) alignments on the TP73 gene was done with Integrative Genomes Viewer (IGV).