Hematopoietic stem cells (HSCs) exhibit considerable cell-intrinsic changes with age. Here, we performed an integrated analysis of transcriptome(RNA-seq) and chromatin accessibility(ATAC-seq) of young and aged HSCs and downstream progenitors.
All original data have been deposited in NCBI(https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE162662), and the codes used for the analyses are stored in this repository and Zenode.
CentOS 7
Human Genome Center, the Institute of Medical Science, the University of Tokyo
(https://gc.hgc.jp/en/sys-const/)
| software | URL |
|---|---|
| bowtie2(2.1.0) | http://bowtie-bio.sourceforge.net/bowtie2/index.shtml |
| Tophat2(2.0.13) | https://ccb.jhu.edu/software/tophat/index.shtml |
| stringtie(1.3.4) | https://ccb.jhu.edu/software/stringtie |
| samtools | http://samtools.sourceforge.net/ |
| bedtools | http://bedtools.readthedocs.io/en/latest/ |
| R (4.0.2) | https://www.r-project.org/ |
| DESeq2 | https://bioconductor.org/packages/ |
| macs2 | https://github.com/macs3-project/MACS |
| Homer | http://homer.ucsd.edu/homer/motif/ |
| sra-toolkit | https://github.com/ncbi/sra-tools |
| Signac | https://satijalab.org/signac/ |
| Seurat | https://satijalab.org/seurat/ |
| Deeptools | https://deeptools.readthedocs.io/en/develop/ |