# RNASeq

This repository the R code to reproduce programmatic figures included in the manuscript:  
**Midena et al**, _Nanoengineered 3D culture substrate enables superior persistence and polyclonal engraftment of genetically engineered hematopoietic stem and progenitor cells_, XXX.

PubMed:  
DOI:  
Raw data: [GSE280536](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE280536)

The 20240208_095535_DGE.rds R object includes all processed data (also raw counts):  

Below, in bullet points the BulkRNAseq workflow adopted in this work:  

- Fastq trimming (3' low quality bases) with TrimGalore (v0.5.0)
- Alignment to GRCh38 (STAR v2.7.0d) according to GenCode primary assembly gene transfer file (.gft)
- Post-Alignment quality control with Qorts (v1.3.5)
- Gene expression quantification with featureCounts (v1.6.3)
- Exploratory data analysis (EDA) and differential expression with DESeq2 (v1.30.0)
- Gene Set Enrichment Analysis and OverRepresentation Analysis with clusterProfiler (v3.8.1)