Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

DNA methylation in progenitor cells: expression study

ABSTRACT: We surveyed DNA methylation profiles of all human RefSeq promoters in relation to gene expression and differentiation in adipose tissue, bone marrow and muscle mesenchymal progenitors, as well as in bone marrow-derived hematopoietic progenitors. We unravel strongly overlapping DNA methylation profiles between adipose stem cells (ASCs), bone marrow mesenchymal stem cells (BMMSCs) and muscle progenitor cells (MPCs), while hematopoietic progenitor cells (HPCs) are more epigenetically distant from MSCs seen as a whole. Differentiation resolves a fraction of methylation patterns common to MSCs, generating epigenetic divergence. RNA was isolated from MSCs isolated from various tissues and from differentiated cells, and hybridized onto Illumina expression arrays. 2-3 replicates per cell type. The supplementary file 'GSE19773_non-normalized.txt' contains the non-normalized data for Samples GSM493884-GSM493894.

ORGANISM(S): Homo sapiens

SUBMITTER: Philippe Collas

PROVIDER: E-GEOD-19773 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Promoter DNA methylation patterns of differentiated cells are largely programmed at the progenitor stage.

Sørensen Anita L AL Jacobsen Bente Marie BM Reiner Andrew H AH Andersen Ingrid S IS Collas Philippe P

Molecular biology of the cell 20100421 12

Mesenchymal stem cells (MSCs) isolated from various tissues share common phenotypic and functional properties. However, intrinsic molecular evidence supporting these observations has been lacking. Here, we unravel overlapping genome-wide promoter DNA methylation patterns between MSCs from adipose tissue, bone marrow, and skeletal muscle, whereas hematopoietic progenitors are more epigenetically distant from MSCs as a whole. Commonly hypermethylated genes are enriched in signaling, metabolic, and ...[more]

PMID: 20410135

Similar Datasets

DNA methylation in progenitor cells: MeDIP study

Project description:We surveyed DNA methylation profiles of all human RefSeq promoters in relation to gene expression and differentiation in adipose tissue, bone marrow and muscle mesenchymal progenitors, as well as in bone marrow-derived hematopoietic progenitors. We unravel strongly overlapping DNA methylation profiles between adipose stem cells (ASCs), bone marrow mesenchymal stem cells (BMMSCs) and muscle progenitor cells (MPCs), while hematopoietic progenitor cells (HPCs) are more epigenetically distant from MSCs seen as a whole. Differentiation resolves a fraction of methylation patterns common to MSCs, generating epigenetic divergence. DNA was isolated from MSCs isolated from various tissues and from differentiated cells, immunoprecipitated using antibodies to 5-methylcytosine, and co-hybridized onto Nimblegen promoter arrays together with input DNA.

2010-05-12 | E-GEOD-19794 | biostudies-arrayexpress

DNA methylation in progenitor cells: MeDIP study

2010-05-12 | GSE19794 | GEO

DNA methylation in progenitor cells: expression study

2010-05-12 | GSE19773 | GEO

Mesenchymal stem cells in local fat depots stimulate breast cancer growth, invasion and desmoplasia

Project description:Studies investigating the role of mesenchymal stem cells (MSCs) in mammary carcinogenesis have almost exclusively relied on isolates from bone marrow aspirates or non-breast fat sources often making the general assumption that all MSCs are alike. Here we conduct the first extensive analysis of human breast adipose MSCs to define similarities and differences to MSCs isolated from non-breast sources (subcutaneous abdominal tissue) and bone marrow.

2011-07-31 | E-GEOD-24433 | biostudies-arrayexpress

The enhancer landscape predetermines the skeletal regeneration capacity of stromal cells [ATAC-seq]

Project description:Mesenchymal stromal cells (MSCs) derived from bone marrow (BM) have stronger potential for endochondral ossification compared to white adipose tissue (WAT)-MSCs, umbilical cord (UC)-MSCs, and skin fibroblasts (FB). We assessed uniquely accessible enhancers facilitating bone regeneration potential.

2023-04-03 | GSE182496 | GEO

The enhancer landscape predetermines the skeletal regeneration capacity of stromal cells [ChIP-seq]

Project description:Mesenchymal stromal cells (MSCs) derived from bone marrow (BM) have stronger potential for endochondral ossification compared to white adipose tissue (WAT)-MSCs, umbilical cord (UC)-MSCs, chondrocytes (CH) and skin fibroblasts (FB). We assessed active regulatory regions facilitating bone-regeneration potential.

2023-04-03 | GSE182495 | GEO

Comparison of mesenchymal stem/stromal cells (MSCs) between human iPS-derived MSC and human primary cultured MSCs

Project description:To characterize and compare XF-iMSC (XenoFree-induced Mesenchymal stem/stromal cells) and various types of MSCs (Adipose-, Bone marrow-, Unbilical cord-derived), we performed a transcriptome analysis of these MSCs

2022-06-22 | GSE206172 | GEO

PRODUCT CHARACTERIZATION AND PRECLINICAL SAFETY OF UMBILICAL CORD MESENCHYMAL STROMAL CELL-DERIVED SMALL EXTRACELLULAR VESICLES

Project description:Mesenchymal stromal cells (MSCs) are multipotent progenitors that can be isolated from different sources, such as the bone marrow, adipose tissue and umbilical cord. The therapeutic potential of MSCs is related to a plethora of immunomodulatory, anti-inflammatory and pro-repair actions, which are at least partially dependent on their secretome. Among the components of MSCs' secretome, EVs have received considerable attention because MSC-EVs exert similar therapeutic properties as their parent cells. Among the different MSC sources for EV production, human umbilical cord MSCs (hUCMSCs) show advantages such as tissue availability, high proliferative profile of the cells and potential beneficial therapeutic effects in a variety of different diseases, such as stroke This study aimed to provide novel insights for future hUCMSC-EVs research and treatment selection. We investigated the influence of the culture and harvesting conditions on the EV proteomic profile, productivity, surface markers expression and evaluated their in vivo biodistribution and toxicity.

2024-05-04 | PXD038850 | Pride

Comprehensive Proteomic Analysis of Exosomes Derived from Human Bone Marrow-, Adipose Tissue-, and Human Umbilical Cord- Mesenchymal Stem Cells

Project description:Mesenchymal stem cells (MSCs)-derived exosomes (exo) have shown comprehensive application prospects over the years. Despite similar functions, exomes from different origins present heterogeneous characteristics and components; however, there are no relevant proteomic analyses. In this study, we isolated exosomes from MSCs, derived from different tissues, by ultracentrifugation. A total of 1014 proteins were detected using a label-free method and analyzed with bioinformatics tools. The results revealed their shared function in the extracellular matrix receptor. Bone marrow-MSCs-derived exosomes showed superior regeneration ability. Likewise, adipose tissue-MSCs-derived exosomes played a significant role in immune regulation. Whereas, umbilical cord-MSCs-derived exosomes were more prominent in tissue damage repair.

2021-04-14 | PXD020948 | Pride

Tissue- and Aging-specific DNA-Methylation Patterns are erased in Mesenchymal Stromal Cells derived from Induced Pluripotent Stem Cells. [Methylation profiling]

Project description:Standardization of mesenchymal stromal cells (MSCs) remains a major obstacle in regenerative medicine. Starting material and culture expansion affect cell preparations and render comparison between studies difficult. In contrast, induced pluripotent stem cells (iPSCs) assimilate towards a ground-state and may therefore give rise to more standardized cell preparations. We reprogrammed bone marrow MSCs into iPSCs which were subsequently re-differentiated towards MSCs. These iPS-MSCs revealed similar morphology, immunophenotype, in vitro differentiation potential, and gene expression profiles as primary MSCs. DNA methylation (DNAm) profiles of iPSCs maintained some donor-specific characteristics, whereas tissue-specific, senescence-associated, and age-related DNAm patterns were erased during reprogramming. iPS-MSCs reacquired senescence-associated DNAm during culture expansion but they remained rejuvenated with regard to age-related DNAm. Overall, iPS-MSCs and MSCs are similar in function but differ in their epigenetic makeup. 12 samples were hybridized to the Illumina Infinium 450k Human Methylation Beadchip

2014-09-24 | E-GEOD-54767 | biostudies-arrayexpress

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