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Unknown,Transcriptomics,Genomics,Proteomics

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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). 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).

ORGANISM(S): Homo sapiens

SUBMITTER: Dirk Paul

PROVIDER: E-GEOD-25716 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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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).

2011-07-01 | GSE25716 | GEO

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

FAIRE-seq in primary human megakaryocytes, erythroblasts and monocytes

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

Homo sapiens

Project description:FAIRE-chip in CHRF-288-11 and K562 cells

| PRJNA133841 | 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

| PRJEB2817 | ENA

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

MEIS1 ChIPseq in CHRF-288-11

Project description:MEIS1 ChIPseq in CHRF-288-11

| PRJEB2815 | ENA

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

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

2006-11-08 | GSE3838 | GEO

Formaldehyde-assisted isolation of regulatory elements with next generation sequencing (FAIRE-seq) in primary human macrophages and foam cells

Project description:We report the open chromatin landscape in primary human macrophages and foam cells using FAIRE-seq CD14+ monocytes were isolated from the blood of 3 healthy volunteers. Monocytes were differentiated into macrophages by culture for 7 days with 50ng/ml macrophage colony stimulating factor and then treated for 48 hours with either oxidized low density lipoprotein (oxLDL) to induce foam cell formation or with a control buffer that lacked oxLDL. The resulting six samples were then subjected to FAIRE-seq using an established protocol (Simon JM, Giresi PG, Davis IJ, Lieb JD. Using formaldehyde-assisted isolation of regulatory elements (FAIRE) to isolate active regulatory DNA. Nature protocols 2012;7:256-67).

2015-04-08 | E-GEOD-54971 | biostudies-arrayexpress

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