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ABSTRACT: Whole genome sequencing of Rab27a/b DKO mice

PROVIDER: PRJNA818694 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR18476629_1.fastq.gz	Fastqsanger.gz
	SRR18476629_2.fastq.gz	Fastqsanger.gz
	SRR18434370_1.fastq.gz	Fastqsanger.gz
	SRR18434370_2.fastq.gz	Fastqsanger.gz

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Mus musculus strain:BL57J/6

Project description:Whole genome sequencing of Rab27a/b DKO mice

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Immune cell infiltration into brain tumor microenvironment is mediated by Rab27-regulated vascular wall integrity

Project description:To investigate the functional role of Rab27a/b in glioblastoma. We established different roles of brain endothelial cells at physoilogical and in tumor states in the genetically mutated Rab27a/b double knock out murine tissues. We performed single cells gene expression profiling analysis using data obtained from RNA-seq from the brains of non-tumor and glioma tissues derived by injection of GL261 tumor cells in Rab27a/b dHET and Rab27a/b dKO mice.

2025-04-15 | GSE268654 | GEO

A multicenter translational biomarker phase II trial of regorafenib in patients with non-resectable pretreated colorectal cancer.

Project description:Primary objectives: The primary objective is to investigate circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS). Primary endpoints: circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS).

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Role of de novo DNA methyltransferases in hematopoietic stem cells (WGBS)

Project description:To investigate the global DNA methylation changes in Dnmt3a-KO and Dnmt3ab-dKO HSCs compared to control HSCs, we performed whole genome bisulfite sequencing Mouse hematopoietic stem cell DNA methylation profiles of control, Dnmt3a-KO and Dnmt3ab-dKO HSCs were generated generated by deep sequencing, in duplicate, using Illumina Hiseq 2000

2014-08-19 | E-GEOD-50780 | biostudies-arrayexpress

Role of de novo DNA methyltransferases in hematopoietic stem cells (WGBS)

Project description:To investigate the global DNA methylation changes in Dnmt3a-KO and Dnmt3ab-dKO HSCs compared to control HSCs, we performed whole genome bisulfite sequencing

2014-08-19 | GSE50780 | GEO

Immune cell infiltration into brain tumor microenvironment is mediated by Rab27-regulated vascular wall integrity

Project description:Aggressive brain tumors often exhibit immunologically ‘cold’ microenvironment, where the vascular barrier impedes effective immunotherapy in poorly understood ways. Tumor vasculature also plays a pivotal role in immunoregulation and antitumor immunity. Here we show that small GTPase Rab27 controls the vascular morphogenesis and permeability for blood content and immune effectors. Thus, in Rab27a/b double knock out (Rab27-dKO) mice, the brain vasculature is abnormally scarce while the blood vessels become dysmorphic and hyperpermeable in the context of brain tumors, including syngeneic glioblastoma. These defects are reflected in rearrangements of endothelial cell subpopulations with underlying diminution of venous endothelial subtype along with changes in gene and protein expression. Notably, Rab27-dKO brain endothelial cells exhibit deficient tight junctions, whereby they enable large-scale extravasation of cytotoxic T cells into the tumor mass. We show that Rab27-regulated vascular T cell infiltration can be exploited to enhance adoptive T cell therapy in syngeneic brain tumors.

2025-06-02 | PXD062939 | Pride

Cancer-cell-secreted miR-9-5p regulates cholesterol homeostasis to promote tumor metastasis [TF TB Rab27AKD miR-9KO]

Project description:To investigate the effects of breast cancer derived EVs on liver metabolism,we inoculated MDA-MB-231,231 /Rab27A KD and 231 /miR-9 KO cells into subcutaneous tumor in NSG mice. We then performed gene expression profiling analysis using data obtained from RNA-seq of liver from mice xenografted MDA-MB-231 cells (tumor bearing) or MDA-MB-231/Rab27A KD cells (231/Rab27A KD) or MDA-MB-231 /miR-9 KO (231/miR-9 KO) and tumor free mice.

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Tet1 and Tet2 mediate epigenetic regulation of developmental genes by protecting DNA methylation canyons against hypermethylation [Bisulfite-Seq]

Project description:This study uses whole methylome sequencing to characterize the methylomes of mouse embryonic fibroblasts (MEF's). Two conditions were analyzed, MEF cells with intact TET1/TET2 enzymes (WT) and MEF cells with TET1/TET2 knocked out (DKO). Our results identify sets of differentially methylated genes which are correlated with TET1/TET2 induced expression changes of the corresponding genes. Whole methylome analysis of M. musculus MEF cells. Two conditions were sequenced and analyzed, the first is wild type (WT), the second (DKO) corresponds to knock-out of TET1 and TET2 enzymes.

2015-12-07 | E-GEOD-58610 | biostudies-arrayexpress

Combined deficiency of Tet1 and Tet2 is compatible with development but leads to epigenetic instability

Project description:Tet enzymes (Tet1/2/3) convert 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC). Tet1 and Tet2 mediate 5hmC generation in mouse embryonic stem cells (ESCs) and various embryonic and adult tissues. To investigate the effects of combined deficiency of Tet1 and Tet2 on pluripotency and development, we have generated Tet1 and Tet2 double knockout (DKO) ESCs and mice. DKO ESCs were depleted of 5hmC, but remained pluripotent with subtle defects in differentiation and changes in gene expression. Double mutant embryos and chimeras exhibited mid-gestation defects and postnatal DKO mice displayed partially penetrant neonatal lethality and stochastic perturbation of imprinting. Viable DKO animals developed normally to adulthood but had reduced 5hmC level, increased 5mC level and lacked 5hmC in germ cells. Nevertheless, DKO mice of both sexes were fertile with females having smaller ovaries and reduced fertility. Our data suggest that both Tet1 and Tet2 contribute to 5hmC levels during development. Their combined loss does not block differentiation and embryogenesis, but leads to partially penetrant embryonic and perinatal abnormalities and compromised viability. Moreover, the presence of substantial levels of 5hmC in DKO embryos and adult mice suggests a significant contribution of Tet3 in hydroxylation of 5mC during development. Methylation patterns in tissue samples from a series of wt and Tet1/Tet2 DKO embryos, neonates and adults were generated using methylated DNA immunoprecipitation with antibodies against 5mC (MeDIP) and 5hmC (hMeDIP) followed by deep sequencing.

2013-02-01 | E-GEOD-42396 | biostudies-arrayexpress

Proteome analysis of thyroid hormone transporter Mct8/Oatp1c1 deficient mice reveals novel dysregulated target molecules involved in locomotor function

Project description:Thyroid hormone (TH) transporter MCT8 deficiency causes severe locomotor disabilities likely due to insufficient TH transport across brain barriers and, consequently, compromised neural TH action. As an established animal model for this disease Mct8/Oatp1c1 double knockout (DKO) mice exhibit strong central TH deprivation, locomotor impairments and similar histo-morphological features as seen in MCT8 patients. The pathways that cause these neuro-motor symptoms are poorly understood. Here, we performed proteome analysis of brain sections comprising cortical and striatal areas of 21-day-old WT and DKO mice. We detected over 2900 proteins by liquid chromatography mass spectrometry, 67 of which were significantly different between the genotypes. Comparison of the proteomic and published RNA-sequencing data showed a significant overlap between alterations in both datasets. In line with previous observations, DKO animals exhibited decreased myelin-associated protein expression and altered protein levels of well-established neuronal TH regulated targets. As one intriguing new candidate, we unraveled and confirmed reduced protein and mRNA expression of Pde10a, a striatal enzyme critically involved in dopamine receptor signaling, in DKO mice. As altered PDE10A activities are linked to dystonia, reduced basal ganglia PDE10A expression may represent a key pathogenic pathway underlying human MCT8 deficiency.

2023-10-27 | PXD045769 | Pride

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