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AThi oHSC ATlo oHSC WES - Identifying clonal differences or differences in mutation burden between autophagy engaging and non-engaging hematopoietic stem cells during mouse aging.

ABSTRACT: AThi oHSC ATlo oHSC WES - Identifying clonal differences or differences in mutation burden between autophagy engaging and non-engaging hematopoietic stem cells during mouse aging.

PROVIDER: PRJNA958170 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR24248804_1.fastq.gz	Fastqsanger.gz
	SRR24248804_2.fastq.gz	Fastqsanger.gz
	SRR24248805_1.fastq.gz	Fastqsanger.gz
	SRR24248805_2.fastq.gz	Fastqsanger.gz
	SRR24248806_1.fastq.gz	Fastqsanger.gz

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AThi oHSC ATlo oHSC WES - Identifying clonal differences or differences in mutation burden between autophagy engaging and non-engaging hematopoietic stem cells during mouse aging.

Project description:We performed paired WES from DNA isolated from AThi and ATlo hematopoietic stem cells (FACS sorted on the basis of GFP marker intensity, 33% GFPlo as ATHi, 33% GFPhi as ATlo) using tail DNA as an internal control to identify somatic mutations. Few mutations were called at a variant allele frequency of ≥ 5% in this bulk sequencing approach, in line with recent results obtained with more sensitive methods. We also observed a high degree of shared mutations between AThi and ATlo oHSCs within each biological replicate, and no conserved mutations across biological replicates. The majority of called mutations were intronic or synonymous single nucleotide variants with limited expected consequences for their encoded proteins. Taken together, these results indicate that differing autophagy levels in oHSCs are not explained by clonal divergence or differential mutagenic burden, nor do they point to mutagenic burden as a driver of oHSC dysfunction in 24-month-old mice. They also do not provide evidence for clonal evolution between AThi and ATlo oHSC subsets.

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yHSC AThi oHSC ATlo oHSC Bulk RNA-seq - Understanding transcriptional changes between autophagy engaging and non-engaging hematopoietic stem cells during mouse aging.

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Project description:Experiment was designed to assess differences in chromatin accessibility across the three indicated HSC populations of interest. By ATAC-seq, we observed large differences in chromatin accessibility between young and old HSCs. However, we found that the chromatin accessibility landscape of AThi and ATlo oHSCs was largely conserved, with no statistically different peaks between the two oHSC subsets and predominantly shared peaks differentially accessible between oHSC subsets and yHSC. Both oHSC subsets had a unidirectional increase in peak accessibility across greater than four thousand statistically significant loci compared to yHSCs, indicating epigenetic de-repression with aging. Pathway analysis of ATAC-seq peaks differing between oHSCs and yHSCs revealed epigenetic poising towards engagement of inflammatory responses, cell stress, and altered metabolic programs in both AThi and ATlo oHSC subsets, with some of the most differentially accessible peaks located in the promoters of genes involved in lipid metabolism. These results suggest that cellular responses associated with oHSC dysfunction are, to some extent, embedded in their epigenetic state.

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