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Unknown,Transcriptomics,Genomics,Proteomics

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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

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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

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

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

Pre-leukemic Cebpa mutant myeloid progenitors

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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

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Deletion of Cebpa from HSCs

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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

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