Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

YHSC and oHSC scRNAseq with oHSC AThi ATlo Index Sorting. Assessing the transcriptional changes associated with autophagy engagement in old hematopoietic stem cells at single cell resolution. [scRNA-Seq]

ABSTRACT: yHSC and oHSC scRNAseq with oHSC AThi ATlo Index Sorting. Assessing the transcriptional changes associated with autophagy engagement in old hematopoietic stem cells at single cell resolution. [scRNA-Seq]

PROVIDER: PRJNA1104666 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

yHSC and oHSC scRNAseq with oHSC AThi ATlo Index Sorting. Assessing the transcriptional changes associated with autophagy engagement in old hematopoietic stem cells at single cell resolution.

Project description:10X genomics single cell analysis of yHSC vs oHSC from Gfplc3/Gfplc3 mice with index sorted SMART-Seq2 sequencing to map AThi oHSC vs ATlo oHSC based on GFP-LC3 marker levels. 10X Genomics data harmonized by nearest neighbor integration and uniform manifold approximation and projection (UMAP) representation distinguished yHSC from oHSC, with the largest transcriptional differences observed in the G0/G1 cell cycle phase cluster. Within oHSCs, AThi oHSCs were almost exclusively observed in the G0/G1 cluster, whereas ATlo oHSCs were spread across the activation continuum, with cells still in the G0/G1 cluster found more proximal to S cluster cells.

2024-05-15 | GSE230281 | GEO

yHSC and oHSC scRNAseq with oHSC AThi ATlo Index Sorting. Assessing the transcriptional changes associated with autophagy engagement in old hematopoietic stem cells at single cell resolution. [scRNA-Seq]

Project description:Index sorted SMART-Seq2 sequencing to map AThi oHSC vs ATlo oHSC based on GFP-LC3 marker levels. Between yHSC and oHSC the largest transcriptional differences observed in the G0/G1 cell cycle phase cluster. Within oHSCs, AThi oHSCs were almost exclusively observed in the G0/G1 cluster, whereas ATlo oHSCs were spread across the activation continuum, with cells still in the G0/G1 cluster found more proximal to S cluster cells.

2024-05-15 | GSE265909 | GEO

yHSC AThi oHSC ATlo oHSC ATAC-Seq - Differences in Chromatin Accessibility in Autophagy engaging vs non-autophagy engaging old hematopoeitic stem cells (HSC) comapred to young HSC.

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.

2024-05-15 | GSE230275 | GEO

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

Project description:We sought to understand the transcriptional profile of autophagy engaging vs non-engaging old hematopoietic stem cells (HSC) referenced against young HSCs. Bulk RNA-seq analyses indicated a large transcriptional divergence between the two oHSC subsets, with pathway analyses of differentially expressed genes (DEG) demonstrating enrichment in inflammatory signaling in AThi oHSCs and in oxidative metabolism signaling in ATlo oHSCs. Ingenuity Pathway Analysis (IPA) inferred that several inflammation-coupled pro-autophagy regulators including p53, Bnip3l, Nupr1, and Nlrp3[22,23], in addition to quiescence enforcing checkpoints FoxO3a, Rb1 and Cdkn1a, were activated in AThi oHSCs.

2024-05-15 | GSE230279 | GEO

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.

2024-05-15 | GSE230270 | GEO

yHSC and oHSC scRNAseq with oHSC AThi ATlo Index Sorting. Assessing the transcriptional changes associated with autophagy engagement in old hematopoietic stem cells at single cell resolution.

Project description:yHSC and oHSC scRNAseq with oHSC AThi ATlo Index Sorting. Assessing the transcriptional changes associated with autophagy engagement in old hematopoietic stem cells at single cell resolution.

| PRJNA958195 | ENA

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

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

| PRJNA958181 | ENA

yHSC AThi oHSC ATlo oHSC ATAC-Seq - Differences in Chromatin Accessibility in Autophagy engaging vs non-autophagy engaging old hematopoeitic stem cells (HSC) comapred to young HSC.

Project description:yHSC AThi oHSC ATlo oHSC ATAC-Seq - Differences in Chromatin Accessibility in Autophagy engaging vs non-autophagy engaging old hematopoeitic stem cells (HSC) comapred to young HSC.

| PRJNA958178 | ENA

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: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.

| PRJNA958170 | ENA

yHSC and oHSC 10X scRNAseq under ad lib, fasted, or fast refeed conditions to evaluate transcriptional impact of transient autophagy engagement in hematopoietic stem cells.

Project description:We observed that 24hr of fasting followed by a 24hr refeeding period improved the regenerative capacity of hematopoietic stem cells isolated from old mice, which was associated with an increase in glycolytic capacity. We sought to evaluate transcriptional changes in yHSC and oHSC compartment following different mouse feeding paradigms at single cell resolution. In yHSCs, AL and F/R groups showed overlapping transcriptional signatures with a distinct pattern for the fasted group. In contrast, in oHSCs, AL and fasted groups showed a strong overlap with a distinct transcriptional signature for the F/R group, reflective of differences in metabolic set points with age.

2024-05-15 | GSE230284 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data