Dataset Information

A comprehensive transcriptome signature of murine hematopoietic stem cell aging

ABSTRACT: We have performed ATAC-seq in highly purified Hematopoeitic Stem cells (HSC, LSK/SLAM) from young (4-5mo) and old (20-24mo) C57BL/6J in order to investigate differences in chromatin accessible sites between these 2 groups.

ORGANISM(S): Mus musculus

PROVIDER: GSE166674 | GEO | 2021/04/02

REPOSITORIES: GEO

ACCESS DATA

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Project description:The infant leukemia-associated gene, Ott1 (Rbm15), has broad regulatory effects on embryonic development and hematopoiesis. Embryonic deletion of Ott1 results in defects to the placenta, spleen and heart. Conditional deletion within the adult hematopoietic compartment demonstrates a requirement in pre-B development and inhibitory roles in myeloid progenitor and megakaryocyte populations. Ott1-deleted bone marrow has an expansion of the Lin- Sca-1+ c-Kit+ (LSK) population which includes the hematopoietic stem cell (HSC) population. Functional HSC testing through competitive repopulation of irradiated recipients demonstrated however, a severe defect in Ott1-deficient HSCs, despite adequate numbers of immunophenotypically identified long term HSCs. Although mice deleted in situ for Ott1 are able to maintain hematopoiesis in steady state over a normal lifetime, but when subjected to proliferative stress, the HSC population loses the self-renewing, G0 fraction and undergoes bone marrow failure. Therefore, Ott1 is required for maintaining HSC quiescence during proliferative stress. To investigate the downstream effects of Ott1 loss, LSK cells were sorted from Ott1-deleted mice and controls then global gene expression profiles were generated through hybridization of total RNA onto microarrays. Gene set enrichment analysis showed significant enrichment with genes altered in aged HSCs. Ott1-deficient HSCs were found to have other aging-associated features such as increased DNA damage, NF kappa B activation and p38Mapk activation, suggesting Ott1 controls pathways also involved in the aging process. Six week old Ott1 flox/null Tg-Mx1cre mice and littermate controls possessing a wild type Ott1 allele were injected with 250 mcg intraperitoneal pIpC every other day for 3 doses. Six weeks post-pIpC, bone marrow was harvested, labeled with lineage markers (B220, CD19, CD4, CD8, CD3, IL7R, Terr119 and Gr-1) and depleted using magnetic beads. The remaining cells were labeled for c-Kit and Sca-1 and the Lin- Sca-1+ c-Kit+ (LSK) population was sorted using a FACSAria cell sorter (BD Biosciences). Approximately 10,000 LSK cells per mouse were isolated from 3 Ott1 flox/null Tg-Mx1cre mice and 3 controls. RNA was extracted using the RNeasy Micro kit (Qiagen, Valencia, CA) and treated with RNAse-free DNAse (Qiagen, Valencia, CA). 50 ng of purified total RNA was linearly amplified using the Ovation RNA amplification system V2 (Nugen, San Carlos, CA) and biotinylated with the FL-Ovation Biotin Module V2 (Nugen, San Carlos, CA) per the supplied protocol. cDNA was then hybridized to Affymetrix Mouse expression array 430A2.0 chips by the Dana Farber Microarray Core Facility (Boston, MA). The raw gene expression values were preprocessed with robust multi-array analysis (RMA) algorithm using BioConductor software.

Dataset Information

A comprehensive transcriptome signature of murine hematopoietic stem cell aging

Dataset's files

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets