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Mus musculus

ABSTRACT: Genome wide map of long noncoding RNA Tug1 binding sites in cultured mouse podocytes

PROVIDER: PRJNA310632 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR3139773.fastq.gz	Fastqsanger.gz
	SRR3139774.fastq.gz	Fastqsanger.gz
	SRR3139775.fastq.gz	Fastqsanger.gz
	SRR3139776.fastq.gz	Fastqsanger.gz
	SRR3139777.fastq.gz	Fastqsanger.gz

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Genome wide map of long noncoding RNA Tug1 binding sites in cultured mouse podocytes

2016-10-24 | GSE77493 | GEO

Genome wide map of long noncoding RNA Tug1 binding sites in cultured mouse podocytes

Project description:We generated a genome wide map of instances where the long noncoding RNA, Tug1, binds to DNA in cultured mouse podocytes under normal glucose conditions using Chromatin-RNA Precipitation coupled with high throughput sequencing (ChIRP-Seq) 48 alternating (even, odd) biotynilated probes were designed to span the full length of Tug1 RNA. Chromatin was prepared from gluteraldehyde crosslinked nuclei from early passage podocytes. Chromatin extracts were duplicated with either even or odd probes. Duplicate samples for Input DNA, Even pulldown (PD) and Odd PD DNA was purified following incubation and supplied for Illumina sequencing by ArrayStar (Rockville, MD).

2016-10-24 | E-GEOD-77493 | biostudies-arrayexpress

Gene expression analysis in mouse podocytes expressing shRNA directed against the long noncoding RNA Tug1

Project description:We generated two mouse podocyte cell lines stably transduced with either a shControl lentiviral construct or a shRNA lentiviral construct designed to target Tug1 RNA to investigate the consequences on the gene expression profile of Tug1 knockdown in differentiated mouse podocytes

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Project description:Gene expression analysis in mouse podocytes expressing shRNA directed against the long noncoding RNA Tug1

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Project description:Cultured Mouse Podocytes

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Increased long noncoding RNA maternally expressed gene 3 contributes to podocyte injury induced by high glucose through regulation of mitochondrial fission

Project description:Excessive mitochondrial fission plays a key role in podocyte injury in diabetic kidney disease (DKD), and long noncoding RNAs (lncRNAs) are important in the development and progression of DKD. However, lncRNA regulation of mitochondrial fission in podocytes is poorly understood. Here, we want to identify how lncRNA changes in human podocytes cultured with high glucose.

2020-07-28 | GSE155188 | GEO

Long non-coding RNA expression profiles in cold-induced injury of mouse livers

Project description:Hepatic injury provoked by cold storage is a major problem affecting liver transplantation, as exposure to cold induces apoptosis in hepatic tissues. Long noncoding RNAs (lncRNAs) are increasingly understood to regulate apoptosis, but the contribution of lncRNAs to cold-induced liver injury remains unknown. Using RNA-seq, we determined the differential lncRNA expression profile in mouse livers after cold storage and found that expression of the lncRNA TUG1 was significantly down-regulated. Over-expression of TUG1 attenuated cold-induced apoptosis in mouse hepatocytes and liver sinusoidal endothelial cells LSECs, in part by blocking mitochondrial apoptosis and ER stress pathways. Moreover, TUG1 attenuated apoptosis, inflammation and oxidative stress in vivo in livers subjected to cold storage. Over-expression of TUG1 also improved hepatocyte function and prolonged hepatic graft survival rates in mice. These results suggest that the lncRNA TUG1 exerts a protective effect against cold-induced liver damage by inhibiting apoptosis in mice, and suggests a potential role for TUG1 as a target for the prevention of cold-induced liver damage in liver transplantation.

2016-01-07 | GSE76609 | GEO

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Project description:Genome wide map of Tfcp2l1 binding sites from mouse kidney

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Hepatocyte nuclear factor 1β binding in E14.5 kidney

Project description:HNF-1β mutations are one of the most common single-gene mutations that underlie kidney developmental disease. Hepatocyte nuclear factor 1β (HNF-1β) is essential for kidney development, but its functions in kidney development are incompletely understood. We identified 8284 HNF-1β binding sites using ChIP-sequencing. The majority of these peaks map to promoter (26%), intron (34%) or distal intergenic regions (37.4%) of the mouse genome. 61% of peaks map to protein coding genes, 12% map to long-noncoding RNAs, and 2% map to miRNAs.

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Genome-wide analysis of WT1-controlled gene expression in podocytes

Project description:We identified binding sites of the Wilms' tumor suppressor protein WT1 in the mouse podocyte genome in vivo by ChIP-seq. Furthermore, we provide a podocyte transcriptome derived from primary podocytes that were isolated by FACS on mouse glomeruli. In short, we show that WT1 activates a highly specific podocyte transcriptome by binding to putative podocyte-specific enhancers and TSS of target genes. Genes bound by WT1 in podocytes include the majority of genes mutated in hereditary podocytopathies as well as components of the slit diaphragm, actin cytoskeleton, extracellular matrix, and within endocytosis pathways. Furthermore, we infer a podocyte TF network from DNA-binding motifs enriched at WT1-bound loci that includes Tead, Lmx1b, Mafb, Tcf21, and Fox-class transcription factors. Examination of transcription factor binding sites for WT1 by ChIP-seq. Transcriptome analysis of podocytes by RNA-seq.

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