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

ABSTRACT: 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).

ORGANISM(S): Homo sapiens

PROVIDER: GSE25716 | GEO | 2011/07/01

SECONDARY ACCESSION(S): PRJNA133841

REPOSITORIES: GEO

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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

Global analysis of kidney gene expression by RNA-Seq of aged CTRP1-deficient mice on high-fat diet

Project description:Aging and obesity profoundly influence organ system health by altering circulating levels of hormones, growth factors, and cytokines. C1q/TNF-related protein 1 (CTRP1) is an endocrine factor with important metabolic, cardiovascular, and renal functions. We sought to determine the impact of CTRP1 deficiency on heart and kidney function in the context of aging and obesity using aged and obese wild-type (WT) and Ctrp1 knockout (KO) mice fed a high-fat diet for eight months or longer. Surprisingly, no differences were observed in blood pressure, heart function, or vascular stiffness between genotypes. Loss of CTRP1, however, resulted in renal enlargement (relative to body weight), reduced urinary creatinine, elevated urinary total protein content and pH, and changes in renal gene expression affecting sugar, fat, and amino acid metabolism pathways. Assessment of glomerular integrity, the extent of podocyte foot process effacement, as well as renal response to water restriction and salt loading did not reveal significant differences between WT and Ctrp1-KO mice. Interestingly, blood platelet, white blood cell, neutrophil, lymphocyte, and eosinophil counts were significantly elevated, whereas mean corpuscular volume and hemoglobin were reduced in Ctrp1-KO mice. Cytokine profiling revealed increased circulating levels of CCL17 and TIMP-1 in KO mice. Compared to a previous study, our current data suggest that chronic high-fat feeding affects renal phenotypes differently than similarly aged mice fed a control low-fat diet, highlighting a diet-dependent contribution of CTRP1 deficiency to age-related changes in renal structure and function.

2020-10-13 | GSE151154 | GEO

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.

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Temporal expression profile of CHRF-288 cell line after phorbol ester stimulation

2006-11-08 | GSE3838 | GEO

MEIS1 ChIPseq in CHRF-288-11

Project description:MEIS1 ChIPseq in CHRF-288-11

| PRJEB2815 | ENA

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

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

2012-01-11 | E-MTAB-858 | biostudies-arrayexpress

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

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Project description:Maps of open chromatin in three primary human blood cell types of the myeloid lineage (megakaryocytes, erythroblasts and monocytes) using the formaldehyde-assisted isolation of regulatory elements method followed by next-generation sequencing (FAIRE-seq). We also generated FAIRE-seq data in the megakaryocytic cell line CHRF-288-11. In addition to our data sets, we retrieved FAIRE-seq data for the erythroblastoid cell line K562 (ENCODE Project Consortium 2012) and pancreatic islets (Gaulton et al. 2010), and reanalyzed these data sets using the same methodology.

2013-04-08 | GSE37916 | 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.

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