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Series GSE162607 Query DataSets for GSE162607
Status Public on Dec 05, 2020
Title Epigenetic traits inscribed in chromatin accessibility in aged hematopoietic stem cells (RNA-seq)
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Hematopoietic stem cells (HSCs) exhibit considerable cell-intrinsic changes with age. Here, we performed an integrated analysis of transcriptome and chromatin accessibility of aged HSCs and downstream progenitors. Alterations in chromatin accessibility preferentially took place in HSCs with aging, which gradually resolved with differentiation. Differentially open accessible regions (open DARs) in aged HSCs showed enrichment of binding motifs of the STAT, ATF, and CNC family transcription factors that are activated in response to external stresses, and most of them comprised active, primed , and inactive enhancers. Genes linked to open DARs showed significantly higher levels of basal expression and their expression reached significantly higher peaks after cytokine stimulation in aged HSCs than in young HSCs, suggesting that open DARs contribute to augmented transcriptional responses under stress conditions. These results indicate that the ongoing and/or history of exposure to external stresses is epigenetically inscribed in HSCs to augment their responses to external stimuli.
Overall design RNA-seq of Young and Aged hematopoietic cells
Contributor(s) Itokawa N, Oshima M, Kuribayashi W, Takayama N, Koide S, Nakajima-Takagi Y, Kazumasa A, Yamazaki S, Eto K, Iwama A
Citation(s) 35577813
Submission date Dec 03, 2020
Last update date May 17, 2022
Contact name Atsushi Iwama
Organization name The Institute of Medical Science, The University of Tokyo
Department Center for Stem Cell Biology and Regenerative Medicine
Lab Division of Stem Cell and Molecular Medicine
Street address 4-6-1, Shirokanedai
City Minato-ku
State/province Tokyo
ZIP/Postal code 108-8639
Country Japan
Platforms (1)
GPL18480 Illumina HiSeq 1500 (Mus musculus)
Samples (32)
GSM4955243 RNA-seq young HSC rep1
GSM4955244 RNA-seq young HSC rep2
GSM4955245 RNA-seq young MPP1 rep1
This SubSeries is part of SuperSeries:
GSE162662 Epigenetic traits inscribed in chromatin accessibility in aged hematopoietic stem cells
BioProject PRJNA682381
SRA SRP295667

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SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE162607_A_CLP-vs-Y_CLP.txt.gz 987.2 Kb (ftp)(http) TXT
GSE162607_A_GMP-vs-Y_GMP.txt.gz 934.7 Kb (ftp)(http) TXT
GSE162607_A_HSC-vs-Y-HSC_itokawa.txt.gz 868.4 Kb (ftp)(http) TXT
GSE162607_A_MEP-vs-Y_MEP.txt.gz 935.6 Kb (ftp)(http) TXT
GSE162607_A_MPP1-vs-Y-MPP1_itokawa.txt.gz 883.3 Kb (ftp)(http) TXT
GSE162607_A_MPP2-vs-Y-MPP2_itokawa.txt.gz 884.8 Kb (ftp)(http) TXT
GSE162607_A_MPP3-vs-Y-MPP3_itokawa.txt.gz 884.9 Kb (ftp)(http) TXT
GSE162607_A_MPP4-vs-Y-MPP4_itokawa.txt.gz 862.7 Kb (ftp)(http) TXT
GSE162607_RNA_seq_gene_count_normalized_by_DESeq2.txt.gz 2.5 Mb (ftp)(http) TXT
GSE162607_Raw_gene_count_matrix.txt.gz 887.1 Kb (ftp)(http) TXT
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