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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcription factor Runx1 cooperates with MyoD and c-Jun to regulate the balance of myoblast proliferation/differentiation [ChIP-seq]

ABSTRACT: Runx1 is expressed in regenerating muscle, specifically in the muscle adult stem cells- the satellite cells. Its exact role and target genes were yet to be identified. We report here Runx1 and potential TF counterparts bind important muscle differentiation related genes Examination of genome-wide chromatin binding of several TFs in primary myoblasts (PM)

ORGANISM(S): Mus musculus

SUBMITTER: kfir Umansky

PROVIDER: E-GEOD-56077 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Transcription factor Runx1 cooperates with MyoD and c-Jun to regulate the balance of myoblast proliferation/differentiation [ChIP-Seq Histone]

Project description:Runx1 is expressed in regenrating muscle, specifically in the muscle adult stem cells- the satellite cells. Its exact role and target genes were yet to be identified. We report here the genome wide histone modification using an active enhancer pattern of H3K4 monomethylation (H3K4me1) and H3K27 acetylation (H3K27ac). Examination of genome wide chromatin binding of several TFs in primary myoblasts (PM)

2015-07-23 | E-GEOD-63572 | biostudies-arrayexpress

Transcription factor Runx1 cooperates with MyoD and c-Jun to regulate the balance of myoblast proliferation/differentiation [ATAC-Seq]

Project description:Runx1 is expressed in regenrating muscle, specifically in the muscle adult stem cells- the satellite cells. Its exact role and target genes were yet to be identified. We report here the genome wide open chromatin paatern, as established by ATAC-seq Examination ofgenome wide pattern naked and therefore trhansposase accecible genomic DNA in primary myoblasts (PM)

2015-07-23 | E-GEOD-63573 | biostudies-arrayexpress

Genome-wide maps of Runx3 bound regions in splenic NK cells activated in vivo with IL-15

Project description:ChIP-seq was conducted using freshly isolated splenic WT NK cells from IL-15/Ra treated mice with anti-Runx3 antibody (Ab) and non-immune serum (NIS) as control. Runx3 and NIS IP from splenic NK cells of IL-15/Ra treated WT mice, isolated by negative selection using NK cell isolation kit (R&D) followed by sorting of NKp46+ cells.

2014-01-22 | E-GEOD-50126 | biostudies-arrayexpress

Transcription factor Runx1 cooperates with MyoD and c-Jun to regulate the balance of myoblast proliferation/differentiation [Expression Study]

Project description:Runx1 is expressed in regenrating muscle, specifically in the muscle adult stem cells- the satellite cells. Its exact role and target genes were yet to be identified This experiment aimed at determining the Runx1 regulated genes in muscle regeneration, specifically in Satellite cells To elucidate the Runx1-mediated transcriptional program involved in early stages of muscle regeneration, we compared gene expression profiles in WT and Runx1f/f primary myobalsts (PM). PM were purified from both genotypes , Total RNA was isolated, reverse-transcribed, fragmented, labeled and hybridized to Affymetrix MoGene 1.0 ST DNA array.

2015-07-23 | E-GEOD-55556 | biostudies-arrayexpress

TLX1 ChIP-Seq in ALL-SIL

Project description:The T-cell leukemia homeobox 1 (TLX1, HOX11) transcription factor is critically involved in the multistep pathogenesis of T-cell acute lymphoblastic leukemia (T-ALL) and often cooperates with NOTCH1 activation during malignant T-cell transformation. However, the exact molecular mechanisms by which these T-cell specific oncogenes cooperate during transformation remain to be established. Here, we used an integrative genomics approach to show that the oncogenic properties of TLX1 are mediated by genome-wide interference with the ETS1 and RUNX1 transcription factors. Partial disruption of ETS1 and RUNX1 activity by ectopic TLX1 expression in immature thymocytes drives repression of T-cell specific super-enhancers and mediates an unexpected transcriptional antagonism with NOTCH1 signaling. These phenomena coordinately trigger a TLX1 driven pre-leukemic phenotype in human thymic precursor cells, which corresponds with the in vivo thymic regression observed in murine TLX1 tumor models, and creates a strong genetic pressure for acquiring activating NOTCH1 mutations as a prerequisite for full leukemic transformation. In conclusion, our results uncover a functional antagonism between cooperative oncogenes during the earliest phases of tumor development and provide novel insights in the multistep pathogenesis of TLX1 driven human leukemia. ChIP-sequencing data was generated for TLX1 in the T-ALL cell line ALL-SIL.

2015-08-05 | E-GEOD-62264 | biostudies-arrayexpress

ChIP-Seq of Klf6 in oligodendrocytes

Project description:We examine the role of Klf6 in oligodendrocyte progenitor cells and determine that Klf6 acts in part through direct regulation of gp130 signaling and nuclear import via importin-Î±5 (ImpÎ±5), a key controller of nuclear trafficking. Examination of Klf6 DNA binding in two different stages of differentiation

2016-04-01 | E-GEOD-79243 | biostudies-arrayexpress

Cell-autonomous function of Runx1 transcriptionally regulates megakaryocytic maturation in mice (ChIP-seq)

Project description:RUNX1 transcription factor (TF) is a key regulator of megakaryocytic development and when mutated is associated with familial platelet disorder and predisposition to acute myeloid leukemia (FPD-AML). We used mice lacking Runx1 specifically in megakaryocytes (MKs) to characterize the Runx1-mediated transcriptional program during advanced stages of MK differentiation. Gene expression and chromatin-immunoprecipitation-sequencing (ChIP-seq) of Runx1 andÂ p300Â identified functional Runx1-bound MK enhancers. Runx1/p300 co-bound regions showed significant enrichment in genes important for MK and platelet homeostasis. Runx1-bound regions were highly enriched in RUNX and ETS motifs and to a lesser extent in GATA motif.Â The data providesÂ the first example of genome-wide Runx1/p300 occupancy in maturating FL-MK,Â unravels the Runx1-regulated program controlling MK maturationÂ in vivoÂ andÂ identifies itsÂ bona fideÂ regulated genes. It advances our understandingÂ of the molecular events that upon mutations in RUNX1 lead to theÂ predisposition to familial platelet disorders and FPD-AML. Examination of RUNX1 and P300 binding in WT mouse megakaryoctye cells using ChIP-Seq. The supplementary 'GSE45372_PeakList.txt' file includes a list of regions identified as binding for P300 or RUNX1 or both.

2013-03-22 | E-GEOD-45372 | biostudies-arrayexpress

Fate changes leading to multipotency of isolated mesenchymal cells [ChIP-Seq]

Project description:Mesenchymal populations include a fraction of cells exhibiting multipotency as well as others with limited differentiation range. It has been assumed that the mesenchymal cellular cascade is topped by a multipotent cell, which gives rise to progeny with diminishing differentiation potentials. Here we show that cultured mesenchymal cells, a priori exhibiting a limited differentiation potential, may gain new capacities and become multipotent following single cell isolation. These fate changes were accompanied by up-regulation of differentiation promoting genes, many of which also became H4K20me1 methylated. Early events in the process included TGFβ and Wnt modulation, and down-regulation of hypoxia signaling. Indeed, hypoxic conditions inhibited the observed cell changes. Overall, cell isolation from neighboring partners caused major molecular changes and particularly, a newly established epigenetic state. It is suggested that MSCs behave non-deterministically and non-hierarchically and should therefore be defined primarily by their capacity to undergo fate changes triggered by environmental cues. MSC 21 population and one of its derived clones (4L.1.4) were grown to confuence, and IP of fragmented DNA using an antibody directed against H4K20ME1, or non-immune serum (control) was done. Pulled DNA was then sequenced.

2014-03-20 | E-GEOD-48544 | biostudies-arrayexpress

Genome-wide map of long non-coding RNA steroid receptor RNA activator (SRA) and its associated RNA heliase p68 in human pluripotent stem cells NTERA2

Project description:We performed Chromatin Isolation by RNA Purification (ChIRP) of SRA and ChIP of p68 following by high-throughput sequencing in NTERA2 cell line. We find that SRA localizes with p68 genome-wide at genes whose function is involved in embryonic development. SRA ChIRP and p68 ChIP of triplicate samples.

2014-06-18 | E-GEOD-58641 | biostudies-arrayexpress

Addiction of t(8;21) and inv(16) AML to native RUNX1 [ChIP-Seq data]

Project description:Cancer cells maintain a sensitive balance between growth-promoting oncogenes and apoptosis inhibitors. We show that WT RUNX1 is required for survival of t(8;21)-Kasumi-1 and inv(16)-ME-1 AML cell lines. The malignant AML phenotype is sustained by a delicate AML1-ETO/RUNX1 balance that involves competition for common DNA binding sites regulating a subset of AML1-ETO/RUNX1 targets. Genomewide sequencing data is included herein: Transcription factors RUNX1 c-terminus and n-terminus which is shared with AML1-ETO were profiled independently), AML1-ETO and AP4 were profiled using ChIP-Seq in Kasumi-1 cells, as well as control ChIP-Seq experiments of non immune serum. Two replicates were performed for each transcription factor profiling and control experiment.

2013-08-18 | E-GEOD-45738 | biostudies-arrayexpress

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