This section of the repository contains the R script used to analyze bulk RNA-seq data generated in the study:
**Conti et al., 2025**
*Senescence and inflammation are unintended adverse consequences of CRISPR-Cas9/AAV6 mediated gene editing in hematopoietic stem cells*.
Published in **Cell Reports Medicine**.
## 🔬 Study Context
Bulk RNA-seq was used to investigate transcriptional changes in human hematopoietic stem and progenitor cells (HSPCs) following CRISPR-Cas9/AAV6-mediated gene editing. The goal was to assess activation of DNA damage response (DDR), senescence, and inflammatory pathways.
## 📂 Repository Content
-`Conti_GE_2025_RNAseq_plots.R`:
The R script used to generate the GSEA-based figures in the manuscript. It includes:
- Differential enrichment analysis of senescence and SASP-related gene sets
- Hallmark pathway analysis (MSigDB)
- Data integration from multiple timepoints (24h and 96h)
- ggplot-based heatmaps and tile plots for NES and p-value visualization
The script assumes that input GSEA result files are organized in the following directories:
-`paired_stranded24h/` — results from 24h timepoint
-`unstrand_96h/` — results from 96h timepoint
## 📊 Data Availability
The RNA-seq data are publicly available on the Gene Expression Omnibus (GEO) under the SuperSeries accession **[GSE244257](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE244257)**.
-`GSE244247`: RNA-seq from day 1 post-editing
-`GSE244248`: RNA-seq from day 4 post-editing
## 📌 Citation
If you use this dataset or code, please cite:
> Conti A., Giannetti K., Midena F., et al. (2025).
> *Senescence and inflammation are unintended adverse consequences of CRISPR-Cas9/AAV6 mediated gene editing in hematopoietic stem cells*.
