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

Molecular alterations in bone marrow mesenchymal stromal cells (BM-MSC) derived from acute myeloid leukemia patients (AML)

ABSTRACT: Genome wide methylation profiling of BM-MSC derived from AML patients in comparison to healthy donor controls using Illumina Infinium HumanMethylation450 Beadchip bisulfit converted genomic DNA extracted from BM-MSC samples (AML n=32) and healthy donor controls (n=12) were hybridized onto an Illumina Infinium HumanMethylation450 Beadchip

ORGANISM(S): Homo sapiens

SUBMITTER: Eva von der Heide

PROVIDER: E-GEOD-79695 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Molecular alterations in bone marrow mesenchymal stromal cells (BM-MSC) derived from acute myeloid leukemia patients (AML)

Project description:Genome wide methylation profiling of BM-MSC derived from AML patients in comparison to healthy donor controls using Illumina Infinium HumanMethylation450 Beadchip

2016-03-30 | GSE79695 | GEO

Transcriptional Alterations in Bone Marrow Mesenchymal Stromal Cells derived from Acute Myeloid Leukemia patients (AML BM-MSC)

Project description:The aim of the study was to get insights into transcriptional alterations in bone marrow mesenchymal stromal cells derived from acute myeloid leukemia patients We compared the global gene expression profile from AML BM-MSC (n=19) to healthy donor (HD) controls (HD BM-MSC n=4) AML BM-MSC and HD BM-MSC were isolated from bone marrow aspirates (see below) and hybridized on an Affymetrix HG-U133 Plus 2.0 GeneChip

2016-07-27 | E-GEOD-84881 | biostudies-arrayexpress

Induced Pluripotent Mesenchymal Stromal Cell Clones Retain Donor-Derived Differences in DNA Methylation Profiles

Project description:Reprogramming of somatic cells into induced pluripotent stem cells (iPSC) is an epigenetic phenomenon. It has been suggested that iPSC retain some tissue-specific memory whereas little is known about inter-individual epigenetic variation of iPSC clones. In this study we have reprogrammed mesenchymal stromal cells (MSC) from human bone marrow by retrovirus-mediated overexpression of OCT-3/4, SOX2, c-MYC, and KLF4. Global DNA-methylation profiles of the initial MSC, MSC-derived iPSC (iP-MSC) and embryonic stem cells (ESC) were then compared using a high density DNA-methylation array covering more than 450,000 CpG sites. Overall, DNA-methylation patterns of iP-MSC and ESC were similar whereas some CpG sites revealed highly significant differences, which were not related to parental MSC. Furthermore, hypermethylation in iP-MSC versus ESC was particularly enriched in developmental genes as well as shore regions next to CpG islands indicating that these differences are not due to tissue-specific memory or random de novo methylation. Subsequently, we searched for CpG sites with donor-specific variation in MSC preparations. These “epigenetic fingerprints” were highly enriched in non-promoter regions and outside of CpG islands – and they were maintained upon reprogramming into iP-MSC. In conclusion, DNA methylation profiles of iP-MSC clones from the same donor were closely related despite heterogeneity of MSC. On the other hand, iP-MSC maintain donor-derived epigenetic differences. In the absence of isogenic controls for disease modeling applications, it would therefore be more appropriate to compare iPSC from different donors rather than a high number of different clones from the same patient. 16 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip

2013-01-09 | E-GEOD-34688 | biostudies-arrayexpress

Pluripotent Stem Cells Escape From Senescence-Associated DNA Methylation Changes [Illumina]

Project description:Pluripotent stem cells evade replicative senescence, whereas other primary cells lose their proliferation and differentiation potential after a limited number of cell divisions M-bM-^@M-^S and this is accompanied by specific senescence-associated DNA methylation (SA-DNAm) changes. Here, we investigate SA-DNAm changes in mesenchymal stromal cells (MSC) upon long-term culture, irradiation-induced senescence, immortalization and reprogramming into induced pluripotent stem cells (iPSC) using high density HumanMethylation450 BeadChips. SA-DNAm changes are highly reproducible and occur particularly in intergenic and non-promoter regions of developmental genes. We demonstrate that ionizing irradiation, although associated with a very similar senescence phenotype, does not affect SA-DNAm. Furthermore, overexpression of the catalytic subunit of the human telomerase (TERT) or conditional immortalization with a doxycycline-inducible system (TERT and SV40 TAg) result in telomere extension but do not influence SA-DNAm. In contrast, we demonstrate that reprogramming into iPSC prevented SA-DNAm changes. Our results indicate that replicative senescence is associated with an epigenetically controlled process which stalls cells in a particular differentiated state, whereas irradiation-induced senescence and immortalization are not causally related to this process. Absence of SA-DNAm in pluripotent cells may play a central role for their escape from cellular senescence. Samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip

2012-09-24 | E-GEOD-37066 | biostudies-arrayexpress

Whole genome methylation profiling of the retinal pigment epithelium of individuals with age-related macular degeneration

Project description:Illumina Infinium HumanMethylation450 BeadChip data from genomic DNA of retinal pigment epithelium from Age-related Macular Degeneration patients or age-matched controls.

2019-08-01 | E-MTAB-7183 | biostudies-arrayexpress

DNA methylome modifications and subtyping in ME/CFS

Project description:Examination of DNA methylome patterns for potential subtypes in a larger cohort of ME/CFS samples using the Illumina Infinium HumanMethylation450 Beadchip Array Bisulfite-converted DNA from 25 samples were hybridised onto the Illumina Infinium HumanMethylation450 Beadchip Array

2017-12-31 | GSE102504 | GEO

Homo sapiens

Project description:Wide methylation analysis in vestibular schwannoma [Infinium HumanMethylation450 BeadChip]

| PRJNA244047 | ENA

DNA methylation of matched primary-metastases medulloblastomas

Project description:DNA methylation was generated from 11 pairs of matched primary-metastases medulloblastoma samples using the Illumina Infinium HumanMethylation450 BeadChip array Total DNA was extracted from primary and metastases medulloblastoma samples, bisulfite converted and hybridized to Illumina Infinium HumanMethylation450 BeadChip according to the manufacturer's instructions.

2015-04-01 | E-GEOD-63669 | biostudies-arrayexpress

Novel DNA methylation targets in oral rinse samples predict survival of patients with oral squamous cell carcinoma

Project description:Epigenome-wide association study (EWAS) of oral rinse samples from a cohort of 82 oral squamous cell carcinoma (OSCC) patients. The Illumina Infinium HumanMethylation450 Beadchip was used to obtain DNA methylation profiles across approximately 450,000 CpGs in oral rinse samples. Bisulphite lsconverted DNA from the 82 oral rinse samples were hybridized to the Illumina Infinium HumanMethylation450 Beadchip

2014-11-25 | E-GEOD-52793 | biostudies-arrayexpress

Secretome analysis of human bone marrow derived mesenchymal stromal cells

Project description:As an essential cellular component of the bone marrow (BM) microenvironment mesenchymal stromal cells (MSC) play a pivotal role for the physiological regulation of hematopoiesis, in particular through the secretion of cytokines and chemokines. Mass spectrometry (MS) facilitates the identification and quantification of a large amount of secreted proteins (secretome), but can be hampered by the false-positive identification of contaminating proteins released from dead cells or derived from cell medium. To reduce the likelihood of contaminations we applied an approach combining secretome and proteome analysis to characterize the physiological secretome of BM derived human MSC. Our analysis revealed a secretome consisting of 315 proteins. Pathway analyses of these proteins revealed a high abundance of proteins related to cell growth and/or maintenance, signal transduction and cell communication thereby representing key biological functions of BM derived MSC on protein level. Within the MSC secretome we identified several cytokines and growth factors such as VEGFC, TGF-β1, TGF-β2 and GDF6 which are known to be involved in the physiological regulation of hematopoiesis. By comparing the peptide patterns of secretomes and cell lysates 17 proteins were identified as candidates for proteolytic processing. Taken together, our combined MS work-flow reduced the likelihood of contaminations and enabled us to carve out a specific overview about the composition of the secretome from human BM derived MSC. This methodological approach and the specific secretome signature of BM derived MSC may serve as basis foffuture comparative analyses of the interplay of MSC and HSPC in patients with hematological malignancies.

2019-02-12 | PXD011643 | Pride

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