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Gene expression changes associated with kinase-inactivated Cdk6 or a complete Cdk6 KO in mouse HSC/MPP1 cells after two rounds of transplantation

ABSTRACT: Gene expression changes associated with kinase-inactivated Cdk6 or a complete Cdk6 KO in mouse HSC/MPP1 cells after two rounds of transplantation

PROVIDER: PRJEB64048 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR11650558.fastq.gz	Fastqsanger.gz
	ERR11650559.fastq.gz	Fastqsanger.gz
	ERR11650560.fastq.gz	Fastqsanger.gz
	ERR11650561.fastq.gz	Fastqsanger.gz
	ERR11650562.fastq.gz	Fastqsanger.gz

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Gene expression changes associated with kinase-inactivated Cdk6 or a complete Cdk6 KO in mouse HSC/MPP1 cells after two rounds of transplantation

Project description:A kinase-inactivated variant of Cdk6 (Cdk6_K43M) was associated with prolonged repopulation potential of mouse lineage-negative, Sca1-positive, cKit-positive, CD150-positive, CD48-negative (HSC/MPP1) cells. In order to understand differences between Cdk6_K43M HSC/MPP1 cells, and HSC/MPP1 cells carrying wild-type Cdk6 (Cdk6_WT) or a complete Cdk6 knock-out (Cdk6_KO) in the context of repopulation the following experiment was performed. Pools of freshly isolated CD45.2-positive HSC/MPP1 cells from mice carrying Cdk6_WT, Cdk6_K43M or Cdk6_KO (all homozygous) were serially transplanted into three CD45.1-positive recipients, per genotype. After two rounds of transplantation, CD45.2-positive HSC/MPP1 cells were isolated using flow cytometry based cell sorting and subjected to library prep for RNA sequencing.

2024-05-22 | E-MTAB-13145 | biostudies-arrayexpress

Single cell RNA Seq to study the effects of kinase-inactivated Cdk6 or a Cdk6 knock-out in the mouse LSK cell compartment

Project description:To understand kinase-dependent and kinase-independent functions of Cdk6 in the hematopoietic stem and progenitor compartment, mouse models carrying wild-type Cdk6 (Cdk6_WT), a homozygous knock-in of a kinase-inactivated variant of Cdk6 (Cdk6_K43M) or a homozygous Cdk6 knock-out (Cdk6_KO) were used. From these mice, lineage-negative, Sca1-positive, c-Kit-positive cells (LSK cells) were isolated by means of flow cytometry cell sorting. 30000 LSK cells per mouse were subjected to library prep for single cell RNA Sequencing using the Chromium NextGem Single Cell 5’ v2 Kit (10x Genomics, Pleasanton, CA, USA)

2024-05-22 | E-MTAB-13149 | biostudies-arrayexpress

Single cell RNA Seq to study the effects of kinase-inactivated Cdk6 or a Cdk6 knock-out in the mouse LSK cell compartment

Project description:Single cell RNA Seq to study the effects of kinase-inactivated Cdk6 or a Cdk6 knock-out in the mouse LSK cell compartment

| PRJEB64052 | ENA

RNA-seq data from VavCre;Jak2+/+; Cdk6+/+, VavCre;Jak2V617F; Cdk6+/+, VavCre;Jak2V617F; Cdk6-/-, VavCre; Jak2+/+; Cdk6-/- murine bone marrow LSK cells and VavCre; Jak2V617F; Cdk6+/+ Palbociclib treated murine bone marrow LSK cells

Project description:We describe a critical role for Cdk6 in JAK2V617F+ MPN evolution. The absence of Cdk6 ameliorates clinical symptoms and prolongs survival of JAK2V617F fl/+ vav-Cre mice. The Cdk6 protein interferes with three hallmarks of disease: besides regulating malignant stem cell quiescence, it promotes NFkB signaling and contributes to cytokine production while inhibiting apoptosis. The treatment with palbociclib did not mirror these effects, showing that the functions of Cdk6 in MPN pathogenesis are largely kinase-independent.

2019-06-10 | GSE123401 | GEO

ChIP sequencing experiment of HA-tagged WT CDK6 or of a C-terminally truncated variant of CDK6 (CDK6 delta-C) in BCR-ABL1 expressing cell lines

Project description:The cell cycle kinase CDK6 interacts with a variety of proteins including cyclins and members of the INK4 and Cip/Kip families. These interactions are thought to involve primarily the N-lobe of the protein. Less is known about the role of the C-lobe for the function of CDK6. In this experiment we assessed the function of the C-lobe in CDK6's interaction with transcriptional complexes. We generated cell lines by retroviral over-expression of BCR-ABL1 in bone marrow cells from CDK6 knock-out mice. We then introduced HA-tagged variants of CDK6 - either wildtype CDK6 (CDK6_WT) or a C-terminally truncated variant of CDK6 lacking the last 32 amino acids of the protein (CDK6_delta-C). ChIP was performed with an antibody against the HA tag. CDK6 KO cell lines were used as controls.

2024-06-30 | E-MTAB-13798 | biostudies-arrayexpress

Gene expression profiling of murine BCR-ABL+ CDK6-wt and CDK6-KO cells

Project description:Dertermination of chromatin accessibility in murine BCR-ABL+ CDK6-wt and CDK6-KO cells

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HSC 5-FU time course

Project description:HSC (Sca+ SP) were isolated from 8-12 week C57B6 mice at various time points after treatment with 5-Fluorouracil. RNA was isolated from 50,000-100,000 FACS sorted cells and subjected to two rounds of T7 based linear amplification using Ambion's Message Amp kit. Two replicates from each time point were analyzed. http://www.plosbiology.org/plosonline/?request=get-document&doi=10.1371%2Fjournal.pbio.0020301 Keywords = HSC Keywords = proliferation Keywords = quiescence Keywords = 5-FU Keywords: time-course

2004-09-28 | GSE1559 | GEO

CDK6 antagonizes p53-induced responses during tumorigenesis

Project description:CDK6 induces a complex transcriptional program to block p53 in hematopoietic cells. CDK6 binds to the promoters of genes including p53-antagonists. Cells lacking CDK6 kinase function are required to mutate p53 to achieve a fully transformed immortalized state.

2018-08-06 | GSE113752 | GEO

CDK6 as key regulator of hematopoietic and leukemic stem cell activation.

Project description:The cyclin-dependent kinases (CDK) CDK6 and CDK4 have redundant functions in regulating cell-cycle progression. We describe a novel role for CDK6 in hematopoietic and leukemic stem cells (HSCs and LSCs) that exceeds its function as cell-cycle regulator. Although hematopoiesis appears regular under steady state conditions Cdk6-/- HSCs do not efficiently repopulate upon competitive transplantation and Cdk6-deficient mice are significantly more susceptible to 5-fluorouracil (5-FU) treatment. We find that activation of HSCs requires CDK6, which interferes with transcription of key regulators including Egr1. The central role of Egr1 is supported by transcriptional profiling of HSCs. The impaired repopulation capacity extends to BCR-ABLp210+ leukemic stem cells. Transplantation with BCR-ABLp210+-infected bone marrow (BM) from Cdk6-/- mice fails to induce disease although recipient mice do harbor LSCs. Egr1 knock-down in cdk6-/- BCR-ABLp210+ LSKs significantly enhances colony formation underlining the importance of the Cdk6-Egr1 axis. Our findings define CDK6 as an important regulator of stem cell activation and as essential component of a transcriptional complex that suppresses Egr1 in HSCs and LSCs. Four-condition experiment, Untreated or polyI:C-treated CDK6-/- cells versus untreated or polyI:C-treated wild-type cells. Biological replicates: 3 untreated replicates, 3 polyI:C-treated replicates.

2015-02-20 | E-GEOD-62012 | biostudies-arrayexpress

RNA-seq data from VavCre Jak2+/+ Cdk6+/+, VavCre Jak2V617F Cdk6+/+, VavCre Jak2V617F Cdk6-/-, VavCre Jak2+/+ Cdk6-/- murine bone marrow LSK cells and VavCre Jak2V617F Cdk6+/+ Palbociclib treated murine bone marrow LSK cells

Project description:RNA-seq data from VavCre Jak2+/+ Cdk6+/+, VavCre Jak2V617F Cdk6+/+, VavCre Jak2V617F Cdk6-/-, VavCre Jak2+/+ Cdk6-/- murine bone marrow LSK cells and VavCre Jak2V617F Cdk6+/+ Palbociclib treated murine bone marrow LSK cells

| PRJNA508629 | ENA

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