Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

13 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-seq comparison of fibro-adipogenic progenitors (FAPs) from wild type, mdx and cardiotoxin-injured mice

ABSTRACT: We purified FAPs from the hind limbs of wild type, mdx and cardiotoxin-injured mice in order to unveil changes in their transcriptomes. RNA was isolated directly from sorted cells and analyzed by 3’ RNA sequencing.

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Mus musculus

SUBMITTER: Gianni Cesareni

PROVIDER: E-MTAB-8040 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Fibro-adipogenic progenitors of dystrophic mice are insensitive to NOTCH regulation of adipogenesis.

Marinkovic Milica M Fuoco Claudia C Sacco Francesca F Cerquone Perpetuini Andrea A Giuliani Giulio G Micarelli Elisa E Pavlidou Theodora T Petrilli Lucia Lisa LL Reggio Alessio A Riccio Federica F Spada Filomena F Vumbaca Simone S Zuccotti Alessandro A Castagnoli Luisa L Mann Matthias M Gargioli Cesare C Cesareni Gianni G

Life science alliance 20190625 3

Fibro-adipogenic progenitors (FAPs) promote satellite cell differentiation in adult skeletal muscle regeneration. However, in pathological conditions, FAPs are responsible for fibrosis and fatty infiltrations. Here we show that the NOTCH pathway negatively modulates FAP differentiation both in vitro and in vivo. However, FAPs isolated from young dystrophin-deficient <i>mdx</i> mice are insensitive to this control mechanism. An unbiased mass spectrometry-based proteomic analysis of FAPs from musc ...[more]

PMID: 31239312

Similar Datasets

p38a MAPK regulates adult muscle stem cell fate by restricting progenitor proliferation during postnatal growth and repair

Project description:We have employed genome-wide transcriptome analysis to characterise the changes in expression that occur between resting and regenerating muscle, and the influence p38-alpha has on these expression profiles.

2014-03-04 | E-MTAB-1533 | biostudies-arrayexpress

Changes in Pdgfra-positive mesenchymal progenitors during muscle regeneration under normal and obese condition.

Project description:Worldwide increases in obese and elderly populations synergistically enhance the incidence of sarcopenia. Accumulation of intermuscular adipose tissue (IMAT) is considered to be a major problem whereby obesity leads to sarcopenic obesity and thus is a promising target for treating this emerging pathological condition. However, while sarcopenic obesity-associated IMAT is suggested to be originated from PDGFRα+ mesenchymal progenitors, processes of their adipogenesis remain largely unexplored. Here we investigated intracellular changes associated with these processes using scRNA-Seq analysis.

2021-01-15 | E-MTAB-9715 | biostudies-arrayexpress

LC-MS/MS analysis of isolated murine brain endothelial cells (BECs) from Arf6-GFP-AAV vs GFP-AAV treated WT mice followed by label-free quantification (LFQ)

Project description:Age-related decline in brain endothelial cell (BEC) function critically contributes to cerebrovascular and neurodegenerative disease. Comprehensive atlases of the BEC transcriptome have become available but results from proteomic profiling are lacking. To gain insights into endothelial pathways affected by aging, we developed a magnetic-activated cell sorting (MACS)-based mouse BEC enrichment protocol compatible with high-resolution mass-spectrometry and analysed the profiles of protein abundance changes across multiple time points between 3 and 18 months of age and identified Arf6 as one of the most prominently downregulated vesicle-mediated transport protein during BEC aging. To better understand the role of Arf6 in BECs, in this experiment we have compared MACS sorted BECs from Arf6-GFP-AAV vs GFP-AAV treated 3-months-old WT mice and found 86 and 110 proteins to be significantly down- and upregulated, respectively. Enrichment analyses of significantly upregulated proteins revealed vesicle-mediated transport, activation of GTPase activity, and ER to Golgi vesicle-mediated transport to be among the most significantly affected biological processes.

2024-02-15 | PXD045006 | Pride

LC-MS/MS analysis of isolated murine brain endothelial cells (BECs) from 3-, 6-, 12-, and 18-months-old mice and Apoe-KO mice at 3 months followed by label-free quantification (LFQ)

Project description:Age-related decline in brain endothelial cell (BEC) function critically contributes to cerebrovascular and neurodegenerative disease. Comprehensive atlases of the BEC transcriptome have become available but results from proteomic profiling are lacking. To gain insights into endothelial pathways affected by aging, we developed a magnetic-activated cell sorting (MACS)-based mouse BEC enrichment protocol compatible with high-resolution mass-spectrometry based proteomics. In this experiment, first we have compared MACS sorted BECs across multiple time points between 3 and 18 months of age. Using unsupervised cluster analysis, we found a segregation of age-related protein dynamics with biological functions including a downregulation of vesicle-mediated transport. Our approach uncovered changes not picked up by transcriptomic studies such as accumulation of vesicle cargo and receptor ligands including Apoe. Therefor in our next proteomics experiment we compared BECs from 3-months-old Apoe-KO and WT mice and found 111 and 103 proteins to be up- and downregulated, respectively. Comparing the BEC proteomic signature of young Apoe-KO mice with the signature of aged (18-months-old) WT mice we found a positive correlation suggesting an accelerating effect of Apoe deficiency on BEC aging.

2024-02-15 | PXD044996 | Pride

LC-MS/MS analysis of isolated murine brain endothelial cells (BECs) from ARF6-KO and WT mice followed by label-free quantification (LFQ)

Project description:Age-related decline in brain endothelial cell (BEC) function critically contributes to cerebrovascular and neurodegenerative disease. Comprehensive atlases of the BEC transcriptome have become available but results from proteomic profiling are lacking. To gain insights into endothelial pathways affected by aging, we developed a magnetic-activated cell sorting (MACS)-based mouse BEC enrichment protocol compatible with high-resolution mass-spectrometry and analysed the profiles of protein abundance changes across multiple time points between 3 and 18 months of age and identified Arf6 as one of the most prominently downregulated vesicle-mediated transport protein during BEC aging. To better understand the role of Arf6 in BECs, in this experiment we have compared MACS sorted BECs from Arf6-KO and WT 3-months-old mice and found 140 and 172 proteins to be significantly down- and upregulated, respectively. Enrichment analyses of significantly downregulated proteins showed mRNA processing to be among the most affected biological processes consistent with our findings on the aged BEC proteome.

2024-02-15 | PXD045004 | Pride

LC-MS/MS analysis of isolated murine brain endothelial cells (EC) and full brain tissue (FT) preparations from 3-months-old mice followed by label-free quantification (LFQ)

2024-02-15 | PXD044993 | Pride

A single cell RNA-seq analysis of cardiac fibroblasts from pressure-overloaded mouse hearts

Project description:To verify the hypothesis that there are distinct subsets of cardiac fibroblasts, we performed single-cell RNA sequencing analysis of cardiac fibroblasts from pressure-overloaded ventricles.

2021-09-22 | E-MTAB-9839 | biostudies-arrayexpress

Immune and transcriptomic response to seasonal influenza vaccination (TIV) in mice

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2016-06-01 | E-GEOD-68771 | biostudies-arrayexpress

RNA-seq of splenic and LN B cells from WT and Gm40600 Tg mice with or without LPS stimulation

Project description:We found that Gm40600 significantly affects plasmablast(PB)-like SP 2/0 cells. To explore the role of Gm40600 in B-cell especially plasma cell (PC) differentiation, we developed Gm40600 Transgenic (Gm40600 Tg) mice. B cells from spleen and lymph nodes (LNs) of WT and Gm40600 Tg mice were sorted by using B220 microbeads. B cells were also stimulated for 3 days by 10 ug/ml LPS. To explore the effect of Gm40600 overexpression on gene expression, we determined mRNA profiles in B cells from WT and Gm40600 Tg mice and LPS-stimulated B cells by RNA-seq. RNA-seq was done with an Illumina HiSeq 2500 instrument at GENEWIZ, Suzhou, China.

2020-07-31 | E-MTAB-8320 | biostudies-arrayexpress

RNA-seq of splenic B cells derived from WT and Itch cKO mice

Project description:We found that the E3 ubiquitin ligase Itch significantly affects early B-cell differentiation. To explore the role of Itch in late B-cell differentiation, we sorted B cells from WT and Itch cKO mice. To explore the effect of Itch deficency on gene expression, we determined mRNA profiles in B cells from WT and Itch cKO mice by RNA-seq. RNA-seq was done with an Illumina HiSeq 2500 instrument at GENEWIZ, Suzhou, China.

2020-03-01 | E-MTAB-8281 | 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