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Transcription profiling by array of human CD34-positive blood cells

ABSTRACT: CD34+ positively isolated from healthy donors (stimulated by G-CSF) with magnetic beads (after blood leukapheresis); CD34- obtained from 10dd cytokine cultured CD34+ Experiment Overall Design: 5 samples of total RNA. Experiment Overall Design: 2 replicates CD34- Experiment Overall Design: 3 replicates CD34+

ORGANISM(S): Homo sapiens

SUBMITTER: Gabriele Bucci

PROVIDER: E-GEOD-11092 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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NA-Seq: a discovery tool for the analysis of chromatin structure and dynamics during differentiation.

Gargiulo Gaetano G Levy Samuel S Bucci Gabriele G Romanenghi Mauro M Fornasari Lorenzo L Beeson Karen Y KY Goldberg Susanne M SM Cesaroni Matteo M Ballarini Marco M Santoro Fabio F Bezman Natalie N Frigè Gianmaria G Gregory Philip D PD Holmes Michael C MC Strausberg Robert L RL Pelicci Pier Giuseppe PG Urnov Fyodor D FD Minucci Saverio S

Developmental cell 20090301 3

It is well established that epigenetic modulation of genome accessibility in chromatin occurs during biological processes. Here we describe a method based on restriction enzymes and next-generation sequencing for identifying accessible DNA elements using a small amount of starting material, and use it to examine myeloid differentiation of primary human CD34+ cells. The accessibility of several classes of cis-regulatory elements was a predictive marker of in vivo DNA binding by transcription fact ...[more]

PMID: 19289091

Similar Datasets

CD34 blood cells

Project description:CD34+ positively isolated from healthy donors (stimulated by G-CSF) with magnetic beads (after blood leukapheresis) CD34- obtained from 10dd cytokine cultured CD34+ Keywords: differentiation

2009-03-01 | GSE11092 | GEO

AMD3100 and G-CSF Mobilize Different CD34+ Cell Populations Based on Gene and miRNA Expression

Project description:Plerixafor (AMD3100) and G-CSF mobilize peripheral blood stem cells (PBSCs) by different mechanisms. A rhesus macaque model was used to compare plerixafor and G-CSF-mobilized CD34+ cells. Three PBSC concentrates were collected from 3 macaques treated with G-CSF, plerixafor, or plerixafor plus G-CSF. CD34+ cells were isolated by immunoselection and were analyzed by global gene and micro RNA (miR) expression microarrays. Unsupervised hierarchical clustering of the gene expression data separated the CD34+ cells into three groups based on mobilization regimen. Plerixafor-mobilized cells were enriched for B cells, T cells and mast cells genes and G-CSF-mobilized cells were enriched for neutrophils, and mononuclear phagocytes (MPs) genes. Genes up-regulated in plerixafor plus G-CSF-mobilized CD34+ cells included many that were not up-regulated by either agent alone. Two hematopoietic progenitor cell miR, miR-10 and miR-126, and a dendritic cell miR, miR-155, were up-regulated in G-CSF-mobilized CD34+ cells. A pre-B cell acute lymphocytic leukemia miR, miR-143-3p, and a T cell miR, miR-143-5p, were up-regulated in plerixafor plus G-CSF-mobilized cells. The composition of CD34+ cells is dependent on the mobilization protocol. Plerixafor-mobilized CD34+ cells include more B, T, and mast cell precursors while G-CSF-mobilized cells have more neutrophil and MP precursors. Three rhesus macaques were given all three mobilization protocols and PBSCs were collected from each of these three animals. Two monkeys were given plerixafor first, one was given G-CSF first and all three were given plerixafor plus G-CSF last. This resulted in 6 samples (CD34+ and CD34- cells from each of the 3 mobilizations) from each of the 3 individual animals (biological replicates).

2009-12-04 | E-GEOD-16936 | biostudies-arrayexpress

Peripheral blood stem cell microRNA profiling

Project description:Mobilized-peripheral blood hematopoietic stem cells (HSCs) have been used for transplantation, immunotherapy, and cardiovascular regenerative medicine. Agents used for HPC mobilization include G-CSF and the CXCR4 inhibitor AMD3100. The HSCs cells mobilized by each agent may contain different subtypes and have different functions. To characterize mobilized HSCs used for clinical applications, microRNA (miRNA) profiling and gene expression profiling were used to compare AMD3100-mobilized CD133+ cells from 4 subjects, AMD3100 plus G-CSF-mobilized CD133+ cells from 4 subjects and G-CSF-mobilized CD34+ cells from 5 subjects. The HSCs were compared to peripheral blood leukocytes (PBLs) from 7 subjects. Keywords: cell type comparison design microRNA (miRNA) profiling were used to compare AMD3100-mobilized CD133+ cells from 4 subjects, AMD3100 plus G-CSF-mobilized CD133+ cells from 4 subjects and G-CSF-mobilized CD34+ cells from 5 subjects. The HSCs were compared to peripheral blood leukocytes (PBLs) from 7 subjects.

2010-04-01 | E-GEOD-11248 | biostudies-arrayexpress

Peripheral blood stem cell gene profiling

Project description:Mobilized-peripheral blood hematopoietic stem cells (HSCs) have been used for transplantation, immunotherapy, and cardiovascular regenerative medicine. Agents used for HPC mobilization include G-CSF and the CXCR4 inhibitor AMD3100. The HSCs cells mobilized by each agent may contain different subtypes and have different functions. To characterize mobilized HSCs used for clinical applications, microRNA (miRNA) profiling and gene expression profiling were used to compare AMD3100-mobilized CD133+ cells from 4 subjects, AMD3100 plus G-CSF-mobilized CD133+ cells from 4 subjects and G-CSF-mobilized CD34+ cells from 5 subjects. The HSCs were compared to peripheral blood leukocytes (PBLs) from 7 subjects. Keywords: cell type comparison design gene expression profiling were used to compare AMD3100-mobilized CD133+ cells from 4 subjects, AMD3100 plus G-CSF-mobilized CD133+ cells from 4 subjects and G-CSF-mobilized CD34+ cells from 5 subjects. The HSCs were compared to peripheral blood leukocytes (PBLs) from 7 subjects.

2010-04-01 | E-GEOD-11247 | biostudies-arrayexpress

Transcription profiling of human CD34 cDNA over-expressing human CD34+ cells

Project description:In order to investigate the role of CD34 antigen in haematopoietic commitment, we overexpressed the human CD34 cDNA in human CD34+ cells by retroviral gene transfer. Experiment Overall Design: In a set of 10 independent experiments, gene transfer efficiency, assessed by flow cytometry analysis of ÎLNGFR positivity, ranged 15 to 30%. Transduced cells were than purified for NGFR expression at day 3 of liquid culture with the retroviral vector. Phenotypic analysis, performed on transduced/NGFR purified cells evidenced that the CD34 transgene was highly expressed at the protein level (80% of LCD34IÎN vs 30% of controls at 5 days post-infection) up to 14 days of liquid culture.

2008-06-18 | E-GEOD-8003 | biostudies-arrayexpress

Transcription profiling of human cord blood derived CD34+ hematopoietic stem/progenitor cells to identifyTGF-beta1 target genes in human dendritic cells (DC).

Project description:CD34+ hematopoietic stem/progenitor cells were isolated from human cord blood and amplified in vitro for 10-14 days in serum-free medium with specific cytokines (Ju et al., Eur. J. Cell Biol. 82, 75-86, 2003; Hacker et al., Nat. Immunol. 4, 380-386, 2003). Cultured progenitor cells were induced to differentiate into DC in RPMI medium supplemented with 10% fetal calf serum, 2 mM L-glutamine, 0.1 microM Beta-mercaptoethanol, 100 U/ml penicillin and streptomycin (GIBCO-BRL) and 500 U/ml GM-CSF, 500 U/ml IL-4 for 6 days with or without 10 ng/ml TGF-beta1 as indicated (0.5x10E6 cells/ml). Every 2 days growth factors were added and cells were maintained at 0.5x10E6 cells/ml cell density. RNA was prepared and subjected to microarray analysis. Experiment Overall Design: Dendritic cells (DC) were treated for various periods of time (4, 16 and 36 hours) with TGF-beta1 (10 ng/ml) or left untreated. Experiment Overall Design: DC untreated Experiment Overall Design: DC + TGF-beta1 for 4 hours Experiment Overall Design: DC + TGF-beta1 for 16 hours Experiment Overall Design: DC + TGF-beta1 for 36 hours

2008-06-13 | E-GEOD-5151 | biostudies-arrayexpress

Transcription profiling of human CD34+ cells and treatment with UTP and CXCL12

Project description:Homing and engraftment of hematopoietic stem cells (HSCs) to the bone marrow (BM) involve a complex interplay between chemokines, cytokines, and non-peptide molecules. Extracellular nucleotides and their cognate P2 receptors are emerging as key-factors of inflammation and related chemotactic responses. In this study, we investigated the activity of extracellular adenosine-triphosphate (ATP) and uridine-triphosphate (UTP) on CXCL12-stimulated CD34+ HSC chemotaxis. In vitro, UTP significantly improved HSC migration, inhibited cell membrane CXCR4 down-regulation of migrating CD34+ cells and increased cell adhesion to fibronectin. In vivo, pre-incubation with UTP significantly enhanced the BM homing efficiency of human CD34+ cells in immunodeficient mice. Pertussis toxin blocked CXCL12- and UTP-dependent chemotactic responses, suggesting that G-protein alpha-subunits (GÎ±i) may provide a converging signal for CXCR4- and P2Y-activated transduction pathways. In addition, gene expression profiling of UTP-treated CD34+ cells and in vitro inhibition assays demonstrated that Rho guanosine 5â-triphosphatases (GTPase) Rac2 and downstream effectors Rho GTPaseâactivated kinases 1 and 2 (ROCK1/2) are involved in UTP-promoted/CXCL12-dependent HSC migration. Our data suggest that UTP may physiologically modulate the migration of HSCs and their homing to the BM, in concert with CXCL12, via the activation of converging signaling pathways between CXCR4 and P2Y receptors, involving GÎ±i proteins and RhoGTPases. Experiment Overall Design: Highly purified CD34+ cells from 6 healthy donors were seeded at 1000000 cells/ml in serum free medium (EX vivo 15) w/o cytokines and treated with 10 mM UTP, 150ng/ml CXCL12, or 10 mM UTP plus 150ng/ml CXCL12 respectively for 24 hours. As a control, CD34+ untreated cells were maintained in the same culture conditions at the same time.

2008-06-13 | E-GEOD-5168 | biostudies-arrayexpress

Transcription profiling of human samples to investigate CD34 antigen role in haematopoietic commitment (GEO Super Series)

Project description:This SuperSeries is composed of the following subset Series:; GSE8002: CD34 gene silencing; GSE8003: CD34 Overexpression Experiment Overall Design: Refer to individual Series

2008-06-18 | E-GEOD-8040 | biostudies-arrayexpress

Transcription profiling of human CD34+ cells cultured under 5% O2 levels to examine granulocytic differentiation

Project description:Little is known about the global transcriptional program underlying granulocytic (G) commitment, differentiation and maturation. Using DNA microarrays and Q-RT-PCR, we examined the transcriptional profile of G differentiation of human CD34-positive hematopoietic stem and progenitor cells cultured with interleukin-3, interleukin-6 granulocyte colony stimulating factor and stem cell factor. The goal this study was to identify genes involved in the various facets of G differentiation including commitment, expansion, differentiation and functional capacity. Experiment Overall Design: G-CSF mobilized peripheral blood CD34-positive cells were cultured with IL-3, IL-6, SCF and G-CSF under 5% O2. Three biological replicate experiments were analyzed and approximately 15% of the samples were technically replicated. Hybridizations were performed in a reference design with all samples labeled with Cy3 and a reference RNA pool labeled with Cy5.

2008-06-14 | E-GEOD-5918 | biostudies-arrayexpress

Transcription profiling of human granulocytic differentiation of primary CD34+ cells cultured under 20% O2 levels

Project description:Little is known about the global transcriptional program underlying granulocytic (G) commitment, differentiation and maturation. Using DNA microarrays and Q-RT-PCR, we examined the transcriptional profile of G differentiation of human CD34-positive hematopoietic stem and progenitor cells cultured with interleukin-3, interleukin-6 granulocyte colony stimulating factor and stem cell factor. The goal this study was to identify genes involved in the various facets of G differentiation including commitment, expansion, differentiation and functional capacity. Experiment Overall Design: G-CSF mobilized peripheral blood CD34-positive cells were cultured with IL-3, IL-6, SCF and G-CSF under 20% O2. Three biological replicate experiments were analyzed and approximately 15% of the samples were technically replicated. Hybridizations were performed in a reference design with all samples labeled with Cy3 and a reference RNA pool labeled with Cy5.

2008-06-14 | E-GEOD-5917 | biostudies-arrayexpress

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