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Effects of TRP53 upregulation by nutlin 3a on the transcriptome of interstitial cell of Cajal (ICC) stem cells

ABSTRACT: Effects of TRP53 upregulation by nutlin 3a on the transcriptome of interstitial cell of Cajal (ICC) stem cells

PROVIDER: PRJNA580218 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10359520_1.fastq.gz	Fastqsanger.gz
	SRR10359520_2.fastq.gz	Fastqsanger.gz
	SRR10359521_1.fastq.gz	Fastqsanger.gz
	SRR10359521_2.fastq.gz	Fastqsanger.gz
	SRR10359522_1.fastq.gz	Fastqsanger.gz

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Effects of TRP53 upregulation by nutlin 3a on the transcriptome of interstitial cell of Cajal (ICC) stem cells

Project description:Interstitial cells of Cajal (ICC) are electrical pacemakers and mediators of neuromuscular neurotransmission in the gastrointestinal tract. Studies in organotypic cultures of intact gastric muscular wall tissues identified Kit(low)Cd44(+)Cd34(+)Insr(+)Igf1r(+) cells as local ICC progenitors (Lorincz et al., Gastroenterology 2008;134:1083-1093). Subsequently, conditionally immortalized Kit(low)Cd34(+) cells were isolated by immunomagnetic and fluorescent cell sorting and serial cloning from the gastric muscular wall of homozygous, 14-day-old H-2Kb-tsA58 and 7-day-old wild-type C57BL/6J mice and shown to share other phenotypic characteristics with in-situ ICC precursors (Bardsley et al., Gastroenterology 2010;139:942-952). ICC and their precursors undergo age-related depletion in mice and humans. These changes are associated with increased protein levels for transformation-related protein 53 (TRP53). This study utilized total RNA-sequencing to investigate the effects of TRP53 upregulation by nutlin 3a treatment (control: nutlin 3b) on the transcriptome of the ICC precursor line D2211B maintained in the verified absence of the SV40 tsA58 large T antigen.

2020-08-24 | GSE139539 | GEO

Transcription profiling of mouse small intestine interstitial cells of Cajal (ICC) from deep muscular plexus and myenteric plexus

Project description:Interstitial cells of Cajal (ICC) have important functions in regulation of motor activity in the gastrointestinal tract. In murine small intestine ICC are gathered in the region of the myenteric plexus (ICC-MY) and within the deep-muscular plexus near the submucosal surface of the circular muscle layer (ICC-DMP). These two classes of ICC have different physiological functions. ICC-MY are pacemaker cells and generate the slow wave electrical rhythmicity of gastrointestinal organs. ICC-DMP form synaptic connections with the varicose nerve terminals of enteric motor neurons and are involved in reception and transduction of motor neurotransmission. In the present study we used recently developed highly selective techniques to isolate the two classes of ICC from enzymatically dispersed intestinal muscles by fluorescence-activated cell sorting. Transcriptional expression of the two functional classes was investigated using DNA microarray analysis. Experiment Overall Design: ICC-DMP and ICC-MY cells were isolated from the murine small intestinal tissues and their transcriptional expression was compared with that of the tunica muscularis tissues. Transcriptional expression profiles of ICC-DMP and ICC-MY were compared to each other also.

2008-06-15 | E-GEOD-7809 | biostudies-arrayexpress

Single-cell RNA-seq of primary human gastric interstitial cells of Cajal

Project description:Gastrointestinal (GI) motility disorders affect millions of people worldwide, yet remain poorly treated due to insufficient knowledge of the molecular networks controlling GI motility. Interstitial cells of Cajal (ICC) are critical GI pacemaker cells, and abnormalities in ICC are implicated in GI motility disorders. Nevertheless, human ICC are poorly characterised, largely due to difficulties in accessing sufficient numbers for research. Two cell surface proteins have been identified as ICC markers: the receptor tyrosine kinase, KIT; and the calcium-activated chloride channel, Anoctamin-1 (ANO1). Anti-KIT antibodies have been used to purify mouse ICC via flow cytometry. Here, we performed single-cell RNA sequencing of KIT-sorted, primary human gastric ICC to better understand networks controlling human ICC biology.

2022-07-04 | E-MTAB-9602 | biostudies-arrayexpress

Transcriptome analysis of a FACS-sorted human intersitial cells of Cajal (ICC) [array]

Project description:Interstitial cells of Cajal (ICC) are electrical pacemakers and mediators of neuromuscular neurotransmission in the gastrointestinal tract. Gastrointestinal stromal tumors (GIST) arise within the ICC lineage due to activating KIT/PDGFRA mutations. In this study we developed a method for isolation of human ICC by immunolabeling and fluorescence-activated cell sorting (FACS). Briefly, human gastric musculature was dissociated and incubated with antibodies against CD45, FCER1A, CD11B, KIT, and CD34. ICC (defined as HP-KIT+CD34- cells), NOT ICC (defined as HP-KIT-CD34- cells), and hematopoietic (HP) cells (defined as HP+ cells) were isolated using FACS. Microarray was performed on ICC, NOT ICC, HP+ cells, and unfractionated gastric tunica muscularis. This study utilized micorarray for the phenotypic characterization of FACS-sorted human ICC, allowing comparison of ICC to other cells of the gastric musculature, including GIST. De-identified human gastric tissues obtained as surgical excess tissue from patients undergoing bariatric operations. This study utilized oligonucleotide microarray analysis to characterize the transcriptome of FACS-sorted human ICC.

2017-02-22 | GSE77839 | GEO

miRNA sequencing profile of isolated Kit+ interstital cells of Cajal (ICC) in Leptin mutant mice

Project description:We report the high-throughput miRNA sequencing of isolated colonic and jejunal Kit+ interstitial cells of Cajal (ICC) from Lepob/ob;KitcopGFP mice, which develop type 2 diabetes, and Lepob/+;KitcopGFP mice which are non-diabetic counterparts and control

2020-12-31 | GSE139578 | GEO

Effect of mutant TRP53 proteins on nutlin-3a treated mouse lymphoma cell lines (RNA-seq)

Project description:Mutations in TRP53, prevalent in human cancers, reportedly drive tumorigenesis through dominant-negative-effects (DNE) over wt TRP53 and neomorphic gain-of-function (GOF) effects. We show that five TRP53 mutants do not accelerate lymphomagenesis on a TRP53-deficient background but strongly synergize with c-MYC over-expression. RNA-seq analysis revealed that mutant TRP53 does not globally repress wt TRP53 function but exerts a DNE with disproportionate impact on subsets of wt TRP53 target genes, particularly those involved in DNA repair, proliferation and metabolism. This reveals that the mutant TRP53 DNE drives tumorigenesis by modulating wt TRP53 function in a manner that is advantageous for neoplastic transformation.

2019-02-19 | GSE111950 | GEO

Transcriptional expression of ICC-DMP and ICC-MY in murine small intestine

2007-11-29 | GSE7809 | GEO

Adult Murine Interstitial Cells of Cajal (ICC) and Small Intestine (Sm Int) Somatic piRNA-like RNA (pilRNA)

Project description:This study annotates the NGS reads in ICC and Sm Int sncRNA libraries. In addition to known sncRNAs, we identified numerous somatic piRNA-like RNAs. This study confirms the expression of pilRNAs in somatic tissues and outlines their major characteristics. ICC and Sm Int were collected from adult mice (C57BL/6). Small RNA was isolated from samples and cDNA libraries were generated for 454 sequencing. Sequences from FastA files were aligned to known sncRNA and the mouse mm9 genome. This was followed by subsequent novel small RNA annotation.

2013-07-15 | E-GEOD-48388 | biostudies-arrayexpress

Transcriptome of Smooth Muscle Cells, Interstitial Cells of Cajal and PDGFRα+ Cells

Project description:Genome scale expression data on absolute numbers of gene isoforms offer essential clues for cellular functions and biological processes. Gastrointestinal (GI) motility is regulated by smooth muscle cells (SMC) closely contacted with interstitial cells of Cajal (ICC) and fibroblast-like PDGFRα+ cells (PαC), forming an electrical syncytium. To uncover genetic identifies and cellular functions of the cells, we isolated these three cell populations from mouse small intestine and colon, obtained the transcriptome for each type of cells, and built each cell type transcriptome browser. To our knowledge, this is the first genetic resource providing a comprehensive reference for all mRNA transcripts expressed in these unique GI cell populations. Integration of these data with the UCSC genome browser revealed novel cell-specific markers, ion channel and transporter isoforms, and unique cellular and biological functions of these cells in GI physiology. Our transcriptome browsers bring new insight into the alternative expression of genes in different types of the cells and provides references for future functional studies. mRNA profiles of SMC, ICC and PDGFRa cells isolated from mouse jejunum and colon were generated by deep sequencing using Illumina Hiseq2000..

2015-07-31 | E-GEOD-57776 | biostudies-arrayexpress

Adult Murine Interstitial Cells of Cajal (ICC) and Small Intestine (Sm Int) Somatic piRNA-like RNA (pilRNA)

2013-07-15 | GSE48388 | GEO