README.md

# 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](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE218462)
- RNA-seq Prime Editing: [GSE218463](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE218463)

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### 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`).