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Unknown,Transcriptomics,Genomics,Proteomics

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FAIRE-seq of the human megakaryocytic cell line CHRF-288-11

ABSTRACT: FAIRE-seq of the human megakaryocytic cell line CHRF-288-11

ORGANISM(S): Homo sapiens

DISEASE(S): megakaryoblastic leukaemia

SUBMITTER: Augusto Rendon

PROVIDER: E-MTAB-858 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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A GWAS sequence variant for platelet volume marks an alternative DNM3 promoter in megakaryocytes near a MEIS1 binding site.

Nürnberg Sylvia T ST Rendon Augusto A Smethurst Peter A PA Paul Dirk S DS Voss Katrin K Thon Jonathan N JN Lloyd-Jones Heather H Sambrook Jennifer G JG Tijssen Marloes R MR Italiano Joseph E JE Deloukas Panos P Gottgens Berthold B Soranzo Nicole N Ouwehand Willem H WH

Blood 20120912 24

We recently identified 68 genomic loci where common sequence variants are associated with platelet count and volume. Platelets are formed in the bone marrow by megakaryocytes, which are derived from hematopoietic stem cells by a process mainly controlled by transcription factors. The homeobox transcription factor MEIS1 is uniquely transcribed in megakaryocytes and not in the other lineage-committed blood cells. By ChIP-seq, we show that 5 of the 68 loci pinpoint a MEIS1 binding event within a gr ...[more]

PMID: 22972982

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MEIS1 ChIPseq in CHRF-288-11

Project description:ChIP-seq of MEIS1 in the human megakaryocytic cell line CHRF-288-11

2012-01-04 | E-MTAB-859 | biostudies-arrayexpress

FAIRE-chip in CHRF-288-11 and K562 cells

Project description:Maps of open chromatin in a megakaryocytic (CHRF-288-11) and an erythroblastoid (K562) cell line using the formaldehyde-assisted isolation of regulatory elements (FAIRE) method. We profiled chromatin structure at 62 non-redundant genetic loci representing all known associations (as of November 2009, CEU population) with 11 cardiovascular traits: coronary artery disease (CAD), (early-onset) myocardial infarction (MI), mean platelet volume (MPV), platelet counts (PLT), platelet signaling (PLS), white blood cell counts (WBC), red blood cell counts (RBC), mean corpuscular volume (MCV), mean corpuscular hemoglobin (MCH), systolic blood pressure (SBP), diastolic blood pressure (DBP), hypertension (HYP). A total of 4 experiments: FAIRE using two different cross-linking times (8 and 12 min) in two cell types (CHRF-288-11 and K562 cells).

2011-07-01 | E-GEOD-25716 | biostudies-arrayexpress

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Project description:Profiling of human megakaryocytic cell lines using genome wide gene expression microarrays

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2006-11-08 | GSE3838 | GEO

MEIS1 ChIPseq in CHRF-288-11

Project description:MEIS1 ChIPseq in CHRF-288-11

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FAIRE-chip in CHRF-288-11 and K562 cells

2011-07-01 | GSE25716 | GEO

Transcription profiling of CHRF-288-11 and primary human megakaryocytic cell cultures provide novel insights into lineage-specific differentiation

Project description:This SuperSeries is composed of the following subset Series: GSE3838: Temporal expression profile of CHRF-288 cell line after phorbol ester stimulation CHRF-288 cells were cultured in the presence of 10 ng/mL phorbol ester (PMA) or equivalent volume of DMSO solvent (0.02%). Unstimulated control cells from time zero (exponentially growing CHRF cells) were also analyzed. For PMA treated legs, only the adherent cells were included in the transcriptional analysis. Two biological replicate experiments were analyzed and approximately one-half of the samples with each experiment were technically replicated. Hybridizations were performed in a reference design with all samples labeled with Cy3 and a reference RNA pool labeled with Cy5. GSE3839: Temporal expression profile of megakaryocytic differentiation primary CD34+ cell culture Experiment G-CSF mobilized peripheral blood CD34-positive cells were cultured with TPO, IL-3, and Flt3-L to induce Mk differentiation. Samples prior to day 5, including uncultured starting cells, were analyzed directly, whereas samples after and including day 5 were positively selected for CD41a expression immediately prior to RNA isolation. Three biological replicate experiments were analyzed and approximately one-half of the samples from each experiment were technically replicated. Hybridizations were performed in a reference design with all samples labeled with Cy3 and a reference RNA pool labeled with Cy5.

2008-01-18 | E-GEOD-8914 | biostudies-arrayexpress

Transcription profiling of human CHRF-288 cell line after phorbol ester stimulation

Project description:Little is known about the global transcriptional program underlying megakaryocytic (Mk) differentiation, maturation, and apoptosis. Using DNA microarrays and Q-RT-PCR, we examined the transcriptional profile of phorbol-ester-induced Mk differentiation of the megakaryoblastic CHRF-288-11 (CHRF) cell line â a model system for investigating megakaryopoiesis. The goals of this study were to (1) verify the megakaryocytic nature of the CHRF cell line at the transcriptional level, and (2) extract novel insights into the key facets of Mk maturation including polyploidization, proplatelet formation, and apoptosis. Experiment Overall Design: CHRF-288 cells were cultured in the presence of 10 ng/mL phorbol ester (PMA) or equivalent volume of DMSO solvent (0.02%). Unstimulated control cells from time zero (exponentially growing CHRF cells) were also analyzed. For PMA treated legs, only the adherent cells were included in the transcriptional analysis. Two biological replicate experiments were analyzed and approximately one-half of the samples with each experiment were technically replicated. Hybridizations were performed in a reference design with all samples labeled with Cy3 and a reference RNA pool labeled with Cy5.

2008-06-12 | E-GEOD-3838 | biostudies-arrayexpress

FAIRE-seq of the human megakaryocytic cell line CHRF-288-11

Project description:FAIRE-seq of the human megakaryocytic cell line CHRF-288-11

| PRJEB2817 | ENA

Genes downstream of p53 mediating its effect on megakaryopoiesis

Project description:In order to examine genes whose expression is altered as a result of the knock-down (KD) of p53, we used gene expression microarray analysis based on the CHRF cell line, a human megakaryoblastic cell line, which upon PMA stimulation undergoes polyploidization, and extends proplatelet-like cytoplasmic protrusions combined with apoptosis. The CHRF cell line has been validated in our laboratory as a good model of in vitro megakaryopoiesis by comparison to hematopoietic stem cells undergoing Mk differentiation. As described, we have previously generated stable p53-KD CHRF cell lines by lentiviral delivery of microRNA-adapted-short hairpin sequences targeting p53 as well as a suitable scrambled-control cell line. For the microarray analysis we utilized the 4x44K whole human genome microarrays from Agilent. This analysis compared the p53-KD CHRF cells against the control CHRF cells in the absence of PMA treatment and on days 1, 3, 5 and 7 after PMA treatment (5 time-points). p53-KD and control samples were hybridized against each other (direct comparison). We carried out two biological replicate experiments, i.e., 10 measurements of gene expression for each microarray probe. Probes from which >50% of measurements were missing were discarded and not included in the analysis of differential expression. Differentially expressed genes were identified using the significance analysis of microarrays (SAM) with a false discovery rate (FDR) of less than 5%, as implemented in the MultiExperiment Viewer (MeV) tool.

2011-07-26 | E-GEOD-30984 | biostudies-arrayexpress

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