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Unknown,Transcriptomics,Genomics,Proteomics

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Analysis of RNA expression changes in normal human hematopoietic stem and progenitor cells

ABSTRACT: RNA expression analysis on purified human long-term and short-term hematopoietic stem cells (LT-HSC, ST-HSC), common myeloid and megakaryocyte-erythrocyte progenitor cells (CMP, MEP) using microarrays. FACS-purified hematopoietic stem and progenitor cell (HSPC) subsets were analyzed for changes in RNA expression using NimbleGen gene expression microarrays. Analysis of RNA expression of bone marrow-derived HSPC subsets of healthy human donors.

ORGANISM(S): Homo sapiens

SUBMITTER: Boris Bartholdy

PROVIDER: E-GEOD-52150 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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HSC commitment-associated epigenetic signature is prognostic in acute myeloid leukemia.

Bartholdy Boris B Christopeit Maximilian M Will Britta B Mo Yongkai Y Barreyro Laura L Yu Yiting Y Bhagat Tushar D TD Okoye-Okafor Ujunwa C UC Todorova Tihomira I TI Greally John M JM Levine Ross L RL Melnick Ari A Verma Amit A Steidl Ulrich U

The Journal of clinical investigation 20140301 3

Acute myeloid leukemia (AML) is characterized by disruption of HSC and progenitor cell differentiation. Frequently, AML is associated with mutations in genes encoding epigenetic modifiers. We hypothesized that analysis of alterations in DNA methylation patterns during healthy HSC commitment and differentiation would yield epigenetic signatures that could be used to identify stage-specific prognostic subgroups of AML. We performed a nano HpaII-tiny-fragment-enrichment-by-ligation-mediated-PCR (na ...[more]

PMID: 24487588

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Analysis of DNA methylation changes in normal human hematopoietic stem and progenitor cells

Project description:DNA methylation analysis on purified human long-term and short-term hematopoietic stem cells (LT-HSC, ST-HSC), common myeloid and megakaryocyte-erythrocyte progenitor cells (CMP, MEP) using HELP arrays. FACS-purified hematopoietic stem and progenitor cell (HSPC) subsets were analyzed for changes in DNA methylation using NimbleGen HELP microarrays. Analysis of DNA methylation of bone marrow-derived HSPC subsets of healthy human donors.

2014-02-07 | E-GEOD-52151 | biostudies-arrayexpress

Analysis of RNA expression and DNA cytosine methylation in healthy human hematopoietic stem and progenitor cells

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2014-02-07 | E-GEOD-52152 | biostudies-arrayexpress

Expression analysis of WASH knockout LT-HSC cells

Project description:Investigation of whole genome gene expression level changes in WASH knockout LT-HSCs, compared to the WASH WT strain. To find the reason that causes LT-HSC abnormal. Gene expression profiling using sorted LT-HSC samples from C57/BL6 strain. Total RNA extracted from WASH control (isolated RNA from WT, IRWT) and knockout mice (IRKO) were quantified by the NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis.Each chip measures the expression level of 44, 170 genes from Mus Musculus.

2014-05-17 | E-GEOD-57741 | biostudies-arrayexpress

Gene expression analysis of four conditions for Puccinia graminis f. sp. tritici

Project description:Puccinia graminis f. sp. tritici is the cause of wheat stem rust. A microarray was designed from genes predicted from the P. graminis f. sp. tritici genome assembly, and gene expression measured for four conditions which include wheat or barley infecting growth stages initiated by urediniospores. mRNA was prepared from fresh urediniospores, uredinospores germinated for 24 hr, wheat seedlings infected with urediniospores for 8 days, and barley seedlings infected with urediniospores for 8 days. The asexual uredinial infection cycle on wheat produces additional urediniospores, which can start new cycles of wheat infection and are readily spread by aerial transport. This expression data is further described in Duplessis et al, Obligate Biotrophy Features Unraveled by the Genomic Analysis of the Rust Fungi, Melampsora larici-populina and Puccinia graminis f. sp. tritici A total of 12 samples were analyzed, including three biological replicates of the four conditions.

2010-12-31 | E-GEOD-25020 | biostudies-arrayexpress

LATE-REPLICATING HETEROCHROMATIN IS CHARACTERISED BY DECREASED CYTOSINE METHYLATION IN THE HUMAN GENOME (expression)

Project description:Heterochromatin is believed to be associated with increased levels of cytosine methylation. With the recent availability of genome-wide, high-resolution molecular data reflecting cytosine methylation or heterochromatic organization, such relationships can be explored systematically. As a well-defined surrogate for heterochromatin, we tested the relationship between DNA replication timing and cytosine methylation in two human cell types, unexpectedly finding that the later-replicating, more heterochromatic regions to be less methylated than early-replicating regions. When we integrated gene expression data into the study, we found that regions of increased gene expression were earlier replicating, as previously identified, and that transcription-targeted cytosine methylation (TTCM) in gene bodies accounts for the positive correlation with early replication. A Self-Organising Map (SOM) approach was able to identify genomic regions with early replication and increased methylation but lacking annotated transcripts, which would have been missed in simple two variable analyses and may encode unrecognized intergenic transcripts. We conclude that the relationship of cytosine methylation with heterochromatin is not simple, and depends on whether the genomic context is tandemly-repetitive sequences often found near centromeres, which are known to be heterochromatic and methylated, or the remaining majority of the genome, where cytosine methylation is targeted preferentially to the transcriptionally-active, euchromatic compartment of the genome. comparison of human fibroblast and GM06690

2011-08-05 | E-GEOD-27518 | biostudies-arrayexpress

Expression analysis of channel catfish anterior kidney at 48h post immersion challenge of vaccinated fish (28 days post vaccination with attenuated Edwardsiella ictaluri) with virulent E. ictaluri

Project description:To determine the global gene transcriptional changes in vaccinated channel catfish anterior kidney after immersion challenge with a virulent Edwardsiella ictaluri compared to sham vaccinated catfish control. The attenuated Edwardsiella ictaluri used for vaccination was Aquavac-ESC which was commercially available, the virulent strain of Edwardsiella ictaluri is the AL93-58 strain. A six chip study using total RNA samples including 3 controls (no vaccination, no challenge) and 3 treated groups (challenge after vaccination). Each RNA sample used for microarray was pooled fish anterior kidney samples (5 fish anterior kidney samples were pooled as one). Each chip measrues the expression level of 65,182 genes. For each sequence, 3 probes were selected. Two copies were prepared on arrays.

2011-10-04 | E-GEOD-32588 | biostudies-arrayexpress

Expression analysis of channel catfish anterior kidney at 48h post immersion vaccination with attenuated Edwardsiella ictaluri

Project description:To determine the global gene transcriptional changes in channel catfish anterior kidney after immersion vaccination with attenuated Edwardsiella ictaluri compared to sham vaccinated catfsih control. The attenuated Edwardsiella ictaluri used for vaccination was Aquavac-ESC which was commercially available. A six chip study using total RNA samples including 3 control and 3 vaccinated samples. Each RNA sample used for microarray was poold fish anterior kidney samples (5 fish anterior kidney samples were pooled as one). Each chip measrues the expression level of 65,182 genes. For each sequence, 3 probes were selected. Two copies were prepared on arrays.

2011-09-09 | E-GEOD-32046 | biostudies-arrayexpress

Molecular characterization of the chromosome 7 in SMZL

Project description:Splenic marginal zone lymphomas (SMZL) are an uncommon type of B-cell non-Hodgkin’s lymphoma (NHL-B) in which no specific chromosomal translocations have been described. In contrast, the most frequent cytogenetic abnormality is the loss of the long arm of chromosome 7 (7q). Previous reports have located this loss in the 7q32 region. In order to better characterize the genomic imbalances in SMZL, molecular studies were carried out in 73 patients with SMZL. To gain insight into the mapping at 7q a tiling array was also used. Our results confirmed the presence of a new region of loss on chromosome 7 in these NHL. In order to better characterize the genomic imbalances in SMZL, molecular studies were carried out in 69 patients with SMZL.

2011-10-10 | E-GEOD-31203 | biostudies-arrayexpress

Gene expression analysis of 35S::JMJ30-HA overexpression transgenic lines grown at 22Â°C under long day conditions

Project description:Analysis of overexpression of JMJ30 in Arabidopsis thaliana (Col). JMJ30 encode the histone demethylases that contain the catalytic JmjC domain. The trimethylation of Histone H3 lysine 27 (H3K27me3) plays a key role in gene repression and developmental regulation. It is actively and dynamically deposited and removed in plants. However, while the H3K27 methyltransferases had been extensively studied, findings on the H3K27 demethylase were few. Here, we show that JMJ30 encodes a H3K27me3 demethylase, and genes up-regulated in 35S::JMJ30-HA transgenic lines are enriched for H3K27me3 targets. Columbia wild-type (Col WT) and 35S::JMJ30-HA transgenic plants were grown at 22Â°C under long day conditions, and seedling samples were collected at 13 day-after-germination (DAG). Two independent sets of WT and 35S::JMJ30-HA seedling mRNA samples were used for this array.

2014-08-31 | E-GEOD-51896 | biostudies-arrayexpress

Expression analysis of genes in Rattus norvegicus lungs at postnatal day 4, 10 and 21 after intrauterine growth restriction induced by low protein diet

Project description:We performed RNA microarray in a low protein diet (LPD) model of IUGR at three key time points of alveolarization process. IUGR and control rat pups had been studied for each time point considered: on postnatal day 4 (P4) before beginning of the alveolarization process, on P10, peak of alveolarization process and on P21 at the end of it. A twelve chip study using total RNA extracted from 14 whole lungs intrauterine growth restricted rat pups compared to 15 controls. RNA was extracted at three key time points of alveolarization in postnatal life. RNA was pooled by groups of 2 ou 3 before analysis.

2014-10-29 | E-GEOD-56956 | biostudies-arrayexpress

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