Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

12 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The Hematopoietic System - Myeloid arm

ABSTRACT: We used microarray to create a normal cell landscape for the myeloid arm of the hematopoietic system. Mononuclear bone marrow cells from heathly donors were enriched for 34+ and hematopoietic stem and progenitor cells were sorted by FACS.

ORGANISM(S): Homo sapiens

SUBMITTER: Nicolas Rapin

PROVIDER: E-GEOD-42519 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Comparing cancer vs normal gene expression profiles identifies new disease entities and common transcriptional programs in AML patients.

Rapin Nicolas N Bagger Frederik Otzen FO Jendholm Johan J Mora-Jensen Helena H Krogh Anders A Kohlmann Alexander A Thiede Christian C Borregaard Niels N Bullinger Lars L Winther Ole O Theilgaard-Mönch Kim K Porse Bo T BT

Blood 20131220 6

Gene expression profiling has been used extensively to characterize cancer, identify novel subtypes, and improve patient stratification. However, it has largely failed to identify transcriptional programs that differ between cancer and corresponding normal cells and has not been efficient in identifying expression changes fundamental to disease etiology. Here we present a method that facilitates the comparison of any cancer sample to its nearest normal cellular counterpart, using acute myeloid l ...[more]

PMID: 24363398

Similar Datasets

ERG promotes the maintenance of hematopoietic stem cells by restricting their differentiation

Project description:To investigate the role of the transcription factor ERG in hematopoiesis we generated Erg heterozygous knockout and conditional Erg knockout mice. We found that several hematopoietic cell types were decreased in these mice. To define Erg downstream target genes in hematopoietic stem cells, we sorted Lineage-, Sca-1+, c-kit+, CD150+, CD48- cells from Erg +/- mice for gene expression analysis. To define Erg downstream target genes in hematopoietic progenitors, we sorted multipotent progenitors (Lineage-, Sca-1+, c-kit+, CD150-) from Erg -/- mice for gene expression analysis. We generated Erg heterozygous knockout mice and provide 3 replicates for wild type (Erg +/+) populations of stem cells (HSC) and 3 replicates for Erg +/- mices. We also generated a conditional Erg knockout mice. We provide 3 replicates for Erg fl/fl and 3 replicates for Erg (-/-) mice.

2015-09-21 | E-GEOD-69873 | biostudies-arrayexpress

Pre-leukemic Cebpa mutant myeloid progenitors

Project description:In this study, we use pre-malignant cells from different Cebpa mutant acute myeloid leukemia (AML) models. We have used conditional KO models (CreLoxP) and isolated hematopoietic cells shortly after induction of recombination, in order to look at pre-leukemic cells, which have acquired the first hit, but not yet undergone full malignant transformation. We have sorted granulocyte-macrophage progenitors (GMPs) and the more immature population pre-granulocyte-macrophages (preGMs) from pre-leukemic mice. We analyzed gene-expression profiles in order to find deregulated genes, which make the cells more prone to undergo transformation.

2013-07-08 | E-GEOD-47813 | biostudies-arrayexpress

Integrative analysis of histone ChIP-seq and gene expression microarray data using Bayesian mixture models

Project description:Histone modifications are a key epigenetic mechanism to activate or repress the expression of genes. Data sets of matched microarray expression data and histone modification data measured by ChIP-seq exist, but methods for integrative analysis of both data types are still rare. Here, we present a novel bioinformatic approach to detect genes that are differentially expressed between two conditions putatively caused by alterations in histone modification. We introduce a correlation measure for integrative analysis of ChIP-seq and gene expression data and demonstrate that a proper normalization of the ChIP-seq data is crucial. We suggest applying Bayesian mixture models of different distributions to further study the distribution of the correlation measure. The implicit classification of the mixture models is used to detect genes with differences between two conditions in both gene expression and histone modification. The method is applied to different data sets and its superiority to a naive separate analysis of both data types is demonstrated. This GEO series contains the expression data of the Cebpa example data set. This data set was derived from sorted Cebpafl/fl and Cebpafl/fl;Mx1Cre murine hematopoietic LSKCD150- 18 post pIpC injections (conditional deletion of Cebpa). The specimens from three Cebpafl/fl and three Cebpafl/fl;Mx1Cre mice were hybridized separately on six Affymetrix Mouse Gene 1.0 ST arrays. Associated histone modification ChIP-seq data is provided by series GSE43007.

2014-02-05 | E-GEOD-49975 | biostudies-arrayexpress

Development of MLL-rearranged leukemia is dependent on a transcriptional program orchestradt by C/EBPα

Project description:Translocations involving the MLL genes are frequently found in Acute Myeloid Leukemia (AML) and are associated with poor prognosis. The MLL fusion proteins act as aberrant transcription factor activating a transcriptional program that transforms the cells, potentially through collaboration with other transcription factors. To investigate this we searched gene expression profiles from patients with MLL-rearranged AML compared with normal hematopoietic progenitor cells for transcriptional regulators and found targets of C/EBPα to be up-regulated in the AML samples, suggesting that C/EBPα might collaborate with MLL fusion proteins in the initial transformation process. We could show that transformation by MLL fusion proteins is dependent on C/EBPα activity both in early progenitors as well as in GMPs. In contrast, C/EBPα was found to be indispensable in an already established leukemia. These results suggest that C/EBPα play an important role in the early transforming event of leukemogenesis. We used microarray to study the early transcriptional changes induced by MLL-ENL expression and we identified a combined C/EBPα / MLL-ENL transcriptional signature. 3 Cebpaflox/flox;Mx1Cre and 3 Cebpaflox/flox;Mx1Cre- mice were sacrificed 14 days after pIpC injection and bone marrow cells were harvested, enriched for cKit-expression and transduced with a pMIG retroviral vector expressing the MLL-ENL fusion protein and GFP. 72 h post first transduction, GFP-positive or negative PreGM cells were sorted.

2013-12-10 | E-GEOD-46534 | biostudies-arrayexpress

Deletion of Cebpa from HSCs

Project description:In this study, we use a conditional mouse model for Cebpa to investigate the significance of C/EBPα in HSCs. The frequency of HSCs is unaltered following deletion of C/EBPα, however, upon serial transplantations of either full BM or purified HSCs, the stem cells and stem cell activity is lost. This is not due to increased proliferation, but rather caused by a shift from quiescence to apoptosis with a resultant exhaustion of the stem cell pool. We identify direct C/EBPα target genes by combining genome-wide C/EBPα ChIP-seq analysis in stem and progenitor cells with gene expression data from HSC with and without C/EBPα. Furthermore, we explore the impact of C/EBPα on active and repressive histone modifications by doing functional genome-wide ChIP-seq analysis of H3K4Me3 and H3K27Me3 in stem and progenitor cells with and without C/EBPα. We have sorted HSCs from 3 Cebpaflox/flox and 4 Cebpaflox/flox;Mx1Cre mice 18 days after pIC injection.

2013-12-10 | E-GEOD-42498 | biostudies-arrayexpress

In Vitro Transformation of Primary Human CD34+ Cells by AML Fusion Oncogenes: Early Gene Expression Profiling Reveals Possible Drug Target in AML

Project description:Different fusion oncogenes in acute myeloid leukemia (AML) have distinct clinical and laboratory features suggesting different modes of malignant transformation. Here we compare the in vitro effects of representatives of major groups of AML fusion oncogenes on primary human CD34+ cells. For the 3 d and 8 d time points, the oncogenes were retrovirally expressed in primary human CD34+ cells, with cells transduced with empty retroviral vector as controls. As retroviral transduction requires days, for the 6 h time point the oncogenes were expressed from a pTracer-CMV/Bsd plasmid using nucleofection. Cells nucleofected with empty pTracer-CMV/Bsd vector were used as a control.

2014-05-01 | E-GEOD-57194 | biostudies-arrayexpress

CC chemokine ligand 18 (CCL18) is associated with disease activity and relapse in ANCA-associated crescentic glomerulonephritis

Project description:Anti neutrophil cytoplasmic antibody (ANCA) associated vasculitis is the most frequent cause of crescentic glomerulonephritis. Histopathologic features and clinical course of the disease are diverse and judgment of disease activity is often limited due to the lack of reliable activity markers. In order to define potentially new molecular or cellular markers in the kidney which may predict clinical outcome, we performed microarray analyses of renal biopsies from patients with ANCA-associated crescentic glomerulonephritis. We correlated expression profiles with clinical data from our prospective study of patients with renal ANCA disease. The CC chemokine ligand 18 (CCL18) was one of the most up-regulated proteins in kidneys of patients with ANCA-associated crescentic glomerulonephritis. CCL18 producing cells in the kidneys were identified as CD68 and CD209 positive myeloid dendritic cells. The density of CCL18 positive cells correlated with the severity of acute tubular injury and with the impairment of renal function. CCL18 protein levels were elevated in serum samples of patients with renal ANCA disease when compared with patients with non- ANCA-associated crescentic glomerulonephritis. Persistence of high CCL18 serum levels correlated with impairment of renal function and the risk of relapsing disease. Therefore, CCL18 might serve as a marker for persistent disease activity and renal relapses in ANCA-associated vasculitis.

2015-09-03 | E-MTAB-1944 | biostudies-arrayexpress

transcriptome analysis of SIRT2 dependent genes modulated during infection by Listeria monocytogenes

Project description:tissue culture cells were treated with an inhibitor to the deacetylase SIRT2 (AGK2) and infected with Listeria monocytogenes

2013-06-01 | E-MEXP-3912 | biostudies-arrayexpress

A methyltransferase EHMT1 controls brown adipose cell fate and adaptive thermogenesis through a PRDM16 complex

Project description:Brown adipose tissue (BAT) dissipates chemical energy in the form of heat, as a defense against hypothermia and obesity. Current evidence indicates that brown adipocytes arise from Myf5+-dermotomal precursors through the action of a PRDM16-C/EBP-_ transcriptional complex; however, the underlying mechanisms that determine lineage specification and maintenance of brown adipose cells remain poorly understood. Here we study the role of euchromatic histone-lysine N-methyltransferase 1 (EHMT1), a brown fat-enriched lysine methyltransferase, as an essential enzymatic component of the PRDM16 transcriptional complex and controls brown adipose cell fate. To identify targets and function of EHMT1, we performed genome-wide gene expression profiling of BAT from control mouce (Ehmt1flox/flox), Ehmt1Myf5 KO mouse (Myf5-Cre+/-; Ehmt1flox/flox) and Ehmt1adipo KO mouse (Adipo-Cre+/-; Ehmt1flox/flox). Loss of EHMT1 in Myf5+ lineage causes a near total loss of brown fat characteristics and induces muscle-selective gene program in vivo. In addition, adipose-specific deletion of EHMT1 by Adipo-Cre leads to a marked reduction of the thermogenic and fat oxidation genes.

2013-11-07 | E-MTAB-1704 | biostudies-arrayexpress

Isolation and Characterization of Clonal Adult Human Brown Adipocytes

Project description:Brown adipose tissue (BAT) evolved in mammals as a natural defence system against hypothermia and obesity. While existence of BAT in adult humans has been recently appreciated, its cellular origin and molecular identity remain elusive due in large to high cellular heterogeneity within adipose tissues. Here we isolated clonal adipocytes from adult human BAT as well as WAT (control) and critically analyzed their transcriptome to identify bona fide BAT markers and its new functions.

2015-01-16 | E-MTAB-2602 | 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