This dataset contains the code used to analyse the single-cell RNA sequencing (scRNA-seq) data, the raw count matrices and all the output obtained from running the code from the manuscript "A Notch trans-activation to cis-inhibition switch underlies hematopoietic stem cell aging" by Matteini et al. scRNA-seq was applied on sorted Lin- Sca1+ cKit+ (LSK) cells from the bone marrow of young and aged C57Bl6 mice and the raw FASTQ files can be found under the GEO accession numbers GSE197070 and GSE269953 (only young and aged controls used in this analysis). The code is in an easily reproducible format, as an Rmarkdown notebook that contains comments that describe all the steps in the analysis. To start reproducing it, download all the files, open the "LSK_scRNAseq_data_analysis.Rmd" file in an Rstudio session and start following its instructions. This repository also contains the supplementary and raw data included in the manuscript.

R, 4.2.1

Seurat, 5.0.1

ggplot2, 3.5.0

patchwork, 1.2.0.9000

R.utils, 2.12.3

clustree, 0.5.1

ggrepel, 0.9.1

clusterProfiler, 4.4.4

enrichplot, 1.16.2