Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-seq of 5 populations from the regenerative region of the brain of young and old mice

ABSTRACT: Five populations from the regenerative region of the brain of young and old mice were sequenced to compare the type and degree of transcriptome-wide change with age between these different populations.

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Mus musculus

SUBMITTER: Dena Leeman

PROVIDER: E-MTAB-5172 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

scRNAseq for bone marrow cells from Cebpαcre/+ R26EYFP/+ SbdsF/F (neutropenia) mice vs Cebpαcre/+ R26EYFP/+ Sbds+/+ (Ctrl) mice

Project description:To delineate the potential molecular mechanisms underlying the communication between neutrophils and NK cells, we performed scRNAseq of the neutropenic bone marrow (12 months after transplantation of Cebpacre/+ Sbds +/+ or F/F cells). To this end, bone marrow cells were subsorted into HSC+MPP (LKS CD48-), HPC1 (LKS CD48+CD150-), B and T cells (B220+, CD3+), NK cells (NK1.1+ NKp46+) and a myeloid ‘rest’ fraction (B220-,CD3-,NKp46- and NK1.1-) and sorted fractions pooled together to obtain robust representation of all bone marrow cell types in the scRNAseq data

2022-12-31 | E-MTAB-12428 | biostudies-arrayexpress

Single-cell profiling of developing mouse adipocyte progenitor cells

Project description:Considerable heterogeneity exists amongst adipose progenitor cells derived from primary visceral white adipose tissue depots. Single cell RNA sequencing, and state of the art analyses, have the power to disentangle this heterogeneity and reveal the underlying development processes that drive adipocyte maturation.

2021-10-02 | E-MTAB-6913 | biostudies-arrayexpress

Tet2-/-Flt3ITD and WT stem and progenitor cells

Project description:The study was a comparison of gene expression using RNA-seq. We analyzed the stem and progenitor cells from WT and Vav-cre+ Tet2fl/fl Flt3-ITD (T2F3) mice. We isolated stem cells LSK (lin- sca+ kit+) and granulocyte-macrophage progenitors GMP (lin- sca- kit+ fcgr+ cd34+) cells from bone marrow. Comparisons were made across genotypes WT vs. T2F3 and cell types LSK vs. GMP. Comparison of WT and Tet2-/-Flt3ITD bone marrow stem and progenitor cells.

2015-05-01 | E-GEOD-57244 | biostudies-arrayexpress

Comparison of aged dormant and active hematopoietic stem cells

Project description:4 months old Scl-tta; H2B-GFP mice where chased with Doxycyclin for 18 months from and then sacrificed at 22 months of age. GFP+ and GFP- cells, or dormant and active HSCs were then sorted and sequenced.

2020-06-25 | E-MTAB-7903 | biostudies-arrayexpress

RNA seq of CD45.2+ Neo1 deficient or wildtype Hematopoietic stem cells, 4 or 15 month after stem cell transplantation

Project description:To study the role of the receptor Neo1 in Hematopoietic stem cells (HSC) we transplanted Neo1 deficient bone marrow and wildtype controls on a CD45.2 background into lethally irradiated CD45.1 recipients. Either 4 or 15 months after transplantation we isolated HSC (Lineage -, Sca-1+, c-Kit+, Cd150+, CD48-, CD34-, CD45.2+) to identify molecular differences due to Neo1 deficiency and found a loss of HSC quiescence and signatures associated with decreased stem cell function.

2020-07-22 | E-MTAB-7902 | biostudies-arrayexpress

Single cell transcriptional profiling of aortic endothelium identifies a hierarchy from endovascular progenitors to differentiated cells

Project description:We performed 3' single-cell RNA-seq using the 10X Genomics Chromium (version 2 chemistry) system on ~6,000 mouse endothelial cells derived from aorta.

2019-05-27 | E-MTAB-7149 | biostudies-arrayexpress

RNA sequencing of primary thymic, bone and skin mesenchymal cells

Project description:Purpose : Elucidate post-natal role of SCA1+ thymic mesenchymal cells (tMCs) and evaluate the functional overlap between thymic, bone and skin MCs. Method : By high speed cell sorting, we isolated primary MCs (Lin- SCA1+ cells) from mouse thymus, bone and skin. We extracted their respective total RNA and compared their transcriptome by high-throughput RNA-sequencing. Results : We found a total of 2036 differentially expressed genes (FC>5, p-adj<0.1 and RPKM>1) between the 3 MC populations. IPA analyses revealed that each MC population was enriched for genes associated to phagocyte chemotaxis. We also denoted 2850 genes with shared expression across MC populations. IPA analysis of those shared genes also revealed an enrichment for genes influencing phagocyte migration, chemotaxis and function. Finally, MC transcriptomes showed that all 3 MC populations were expressing genes associated with hematopoietic stem and progenitor cell (HSPC) support, strongly suggesting that MCs from thymic, bone and skin all possess the ability to support HSPCs. Conclusion : Overall, our study highlighted 3 potential novel roles for tMCs : 1) Promoting macrophage/monocyte chemotaxis, 2) Enhacing the apoptotic cell clearance process and 3) setting an inviting niche for hematopoietic progenitors. These novel biological roles for tMCs could have substantial effets on thymic biology. Finally, our RNA-seq data offer a valuable resource to the community that can be mined to explore multiple questions related mesenchymal cell biology. Transcriptome comparison between MC populations

2016-02-26 | E-GEOD-73175 | biostudies-arrayexpress

ATAC-seq of mouse luminal progenitors isolated from wild-type or Blg-Cre;Brca1f/f;p53+/- mouse models

Project description:One of the major hurdles for the early detection of cancer is our poor understanding of tumour initiating events. Historically, cancer research has focused on histological and molecular characterisation of established tumours which has led to the identification of hundreds of putative driver mutations. It is currently unclear how these genetic aberrations impact the cell state of nascent tumour cells and their microenvironment. BRCA1 driven triple negative breast cancer (TNBC) for example has been shown to arise from luminal progenitor cells yet little is known about how BRCA1 loss-of-function (LOF) and concomitant mutations affect the luminal progenitor cell state. This repository contains ATAC-sequencing dataset of luminal progenitors isolated from 6-months old Brca1/p53 and wild-type mice. This data was used to show that the perturbation of Brca1/p53in luminal progenitors induces an aberrant alveolar differentiation pre-malignancy. Unlike alveolar differentiation occurring during gestation, this process is cell autonomous and characterised by the dysregulation of transcription factors driving alveologenesis. The ATAC-sequencing data supports a model where transcriptional and epigenetic changes driven by Brca1/p53 inadvertently promote a differentiation program hardwired in luminal progenitors, highlighting the deterministic role of the cell of origin and offering a potential explanation for the tissue specificity of BRCA1 tumours.

2021-02-02 | E-MTAB-10054 | biostudies-arrayexpress

Expression profiling by high throughput sequencing

Project description:Innate immune cells control acute eosinophilic lung inflammation induced by cystein proteases. Here we characterize the dynamic change of gene expression profile in basophils, natural helper cells and eosinophils during lung inflammation via cystein protease Examination of mRNA levels in individual cell populations, basophils, natural helper cells and eosinophils of the lung from naïve mice and papain treated mice.

2014-03-28 | E-GEOD-56292 | biostudies-arrayexpress

RNA-seq of mouse Paneth and Lgr5 expressing intestinal stem cells (ISCs)

Project description:The experiment shows the aging related expression changes in Paneth and Lgr5Hi cells between young and old mice. These expression changes are related to the role of stem cell niche in aging and regeneration of intestinal epithelium.

2019-07-08 | E-MTAB-7916 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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