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Analysis of the DNA methylome and transcriptome in granulopoiesis reveal timed changes and dynamic enhancer methylation [expression]

ABSTRACT: The study investigated the changes in DNA-methylation and gene expression during granulopoiesis. To this end CMP, GMP, PMC and PMN cell populations were isolated by FACS from bonemarrow from healty donors and analysed by CAGE as well as expression and DNA microarrays total RNA was isolated from CMP, GMP, PMC and PMN cells from human bonemarrow from 5 healty donors.

ORGANISM(S): Homo sapiens

SUBMITTER: Karl Ekwall

PROVIDER: E-GEOD-49883 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Analysis of the DNA methylome and transcriptome in granulopoiesis reveals timed changes and dynamic enhancer methylation.

Rönnerblad Michelle M Andersson Robin R Olofsson Tor T Douagi Iyadh I Karimi Mohsen M Lehmann Sören S Hoof Ilka I de Hoon Michiel M Itoh Masayoshi M Nagao-Sato Sayaka S Kawaji Hideya H Lassmann Timo T Carninci Piero P Hayashizaki Yoshihide Y Forrest Alistair R R AR Sandelin Albin A Ekwall Karl K Arner Erik E Lennartsson Andreas A

Blood 20140326 17

In development, epigenetic mechanisms such as DNA methylation have been suggested to provide a cellular memory to maintain multipotency but also stabilize cell fate decisions and direct lineage restriction. In this study, we set out to characterize changes in DNA methylation and gene expression during granulopoiesis using 4 distinct cell populations ranging from the oligopotent common myeloid progenitor stage to terminally differentiated neutrophils. We observed that differentially methylated si ...[more]

PMID: 24671952

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Analysis of the DNA methylome and transcriptome in granulopoiesis reveal timed changes and dynamic enhancer methylation [expression]

2014-04-29 | GSE49883 | GEO

Analysis of the DNA methylome and transcriptome in granulopoiesis reveal timed changes and dynamic enhancer methylation

Project description:The study investigated the changes in DNA-methylation and gene expression during granulopoiesis. To this end CMP, GMP, PMC and PMN cell populations were isolated by FACS from bone marrow from healthy donors and analysed by CAGE as well as expression and DNA microarrays. Bisulphite converted DNA from biological triplicate samples of CMP, GMP, PMC and PMN cell poplulations were hybridised to the Illumina Infinium 450k Human Methylation Beadchip.

2014-03-27 | E-GEOD-50797 | biostudies-arrayexpress

Analysis of the DNA methylome and transcriptome in granulopoiesis reveal timed changes and dynamic enhancer methylation

2014-03-27 | GSE50797 | GEO

Next Generation Sequencing analysis to compare expression patterns of myeloid progenitors in healthy donors and MDS patients

Project description:Transcriptional changes occurring in the CMPs and GMPs of untreated "CMP pattern" and "GMP pattern" MDS patients were compared with the transcriptional profile of CMPs and GMPs from healthy donors

2022-01-02 | GSE178840 | GEO

Gene expression profiles of human hematopoietic progenitors [BLUEPRINT hematopoietic progenitors]

Project description:An optimized whole genome bisulfite sequencing protocol (µWGBS, Farlik et al. 2015 Cell Reports) was used to establish DNA methylation profiles of FACS-purified stem and progenitor cells types of the human blood lineage. Most cell types were sorted from the peripheral blood of three donors each (43 donors total) with eight pools of ten cells, two pools of 50 cells, and one pool of 1000 cells. Additionally, two cell types (HSC, MPP) were sorted from bone marrow, fetal liver, and cord blood; single-cell methylome sequencing (scWGBS, Farlik et al. 2015 Cell Reports) was done for selected cell types (HSC, MPP, CMP, GMP, CLP, MLP0); and gene expression profiling using the Smart-seq2 protocol (Picelli et al. 2013 Nature Methods) was done on all stem/progenitor cell types (HSC, MPP, CMP, MEP, GMP, CLP, MLP0, MLP1, MLP2, MLP3).

2016-11-06 | GSE87195 | GEO

DNA methylation profiles of human hematopoietic progenitors [BLUEPRINT hematopoietic progenitors]

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Expression data from G0 versus G4/G5 CMP/GMP

2015-04-09 | GSE62278 | GEO

Expression data from G0 versus G4/G5 CMP/GMP

Project description:Telomere dysfunctional CMP/GMP have deregulated pathways that are associated with DNA damage signaling We compared differentially expressed genes in the G4/G5 CMP relative to the G0 control to identify pathways that may affect CMP differentiation. Bone marrow CMP and GMP cells were sorted from two paired pools of G0 TERTER/+ or G4/G5 TERTER/ER mice (5,000-20,000 cells per sample) using the Influx Cell Sorter. Every paired pool includes CMP or GMP sorted from 4 age and gender matched G0 or G4/G5 mice. RNA from the respective sorted cells was extracted using Trizol (Ambion) and profiled on 2100 Bioanalyzer (Agilent). Gene expression profiling was performed at the Sequencing and Non-coding RNA Program at MD Anderson Cancer Center. Briefly, the GeneChip® 3 IVT Express Kit (Affymetrix) was used to generate biotin-labeled cRNA, which were purified and fragmented, before target hybridization on the GeneChip® Mouse Genome 430 2.0 Array (Affymetrix) according to the manufacturer's instructions. Affymetrix raw data (CEL files) were normalized using Affymetrix Microarray Suite (MAS) version 5.0 using a TGT=100. Paired pools used in the study were: CMP pool 1: G0-1 and G4/5-1 CMP pool 2: G0-2 and G4/G5-2 GMP pool 1: G0-1 and G4/G5-1 GMP pool 2: G0-2 and G4/G5-2

2015-04-09 | E-GEOD-62278 | biostudies-arrayexpress

Transcription profiles of WT and CreER-Raptor-flox/flox common myeloid progenitors (CMP), granulocyte-macrophage progenitor (GMP), or lineage negative (Lin-) stimulated with M-CSF for 12 hours

Project description:Myelopoiesis is impaired in Raptor-deleted mice (CreER-Rptor-flox/flox). To evaluate the transcriptional changes in myeloid precursors , we isolated CMP (Lin–Sca-1–c-Kit+CD34+FcγRII/IIImid), GMP (Lin–Sca-1–c-Kit+CD34+FcγRII/IIIhigh) and Lin (B220, Ly6C, Ly6G, CD3, Ter-119) negative cells (Lin–) from bone marrow of WT or CreER-Rptor-flox/flox mice. RNA was isolated from CMP and GMP immediately after sorting and Lin- cells were cultured for 12 hours with M-CSF (10 ng/mL) in 10% FBS and 1% P/S DMEM before RNA isolation. We used microarrays to compare the global transcription profiles of CMP, GMP, or Lin– stimulated with M-CSF for 12 hours from WT and CreER-Raptor-flox/flox mice.

2017-07-31 | GSE100256 | GEO

Gene expression analysis of early haematopoietic progenitors

Project description:The common myelo-erythroid progenitor (CMP) was subdivided based on expression of CD27. To understand the relationship between the various CD27 fractions of the CMP and downstream progenitors (granulocyte-monocyte progenitor, GMP, and megakaryocyte-erythroid progenitor, MEP), genome-wide transcriptional analysis was used.

2016-10-31 | GSE33937 | GEO

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