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Series GSE162570 Query DataSets for GSE162570
Status Public on Dec 05, 2020
Title Epigenetic traits inscribed in chromatin accessibility in aged hematopoietic stem cells (ChIP-seq H3K27me3 H3K4me3)
Organism Mus musculus
Experiment type Genome binding/occupancy 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 H3K4me3, H3K27me3, and H2AK119ub profiling by ChIP-seq
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 02, 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 (16)
GSM4954696 young H3K27me3 HSC rep1
GSM4954697 young HSC input rep1
GSM4954698 young H3K27me3 HSC rep2
This SubSeries is part of SuperSeries:
GSE162662 Epigenetic traits inscribed in chromatin accessibility in aged hematopoietic stem cells
BioProject PRJNA682224
SRA SRP295572

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Supplementary file Size Download File type/resource
GSE162570_RAW.tar 1.9 Gb (http)(custom) TAR (of BW)
GSE162570_pooled_Aged_HSC_K119ub_peaks.broadPeak.gz 417.2 Kb (ftp)(http) BROADPEAK
GSE162570_pooled_Aged_HSC_K27me3_peaks.broadPeak.gz 481.2 Kb (ftp)(http) BROADPEAK
GSE162570_pooled_Aged_HSC_K4me3_peaks.narrowPeak.gz 115.4 Kb (ftp)(http) NARROWPEAK
GSE162570_pooled_Young_HSC_K119ub_peaks.broadPeak.gz 63.0 Kb (ftp)(http) BROADPEAK
GSE162570_pooled_Young_HSC_K27me3_peaks.broadPeak.gz 1.5 Mb (ftp)(http) BROADPEAK
GSE162570_pooled_Young_HSC_K4me3_peaks.narrowPeak.gz 198.3 Kb (ftp)(http) NARROWPEAK
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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