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MiRNA sequencing of pheochromocytomas (172 samples)

ABSTRACT: miRNA sequencing of pheochromocytomas (172 samples)

PROVIDER: PRJEB7952 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR696685.fastq.gz	Fastqsanger.gz
	ERR696686.fastq.gz	Fastqsanger.gz
	ERR696687.fastq.gz	Fastqsanger.gz
	ERR696688.fastq.gz	Fastqsanger.gz
	ERR696689.fastq.gz	Fastqsanger.gz

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miRNA sequencing of pheochromocytomas (172 samples)

Project description:A Carte d'Identitite des Tumeurs (CIT) project from the french Ligue Nationale Contre le Cancer (http://cit.ligue-cancer.net): Pheochromocytomas (PCC) and paragangliomas (PGL) are neural crest-derived tumors. We performed the integrated genomic analysis of a collection of PCC/PGL from the French COMETE network using SNP arrays, whole-exome sequencing, DNA methylation arrays, mRNA expression arrays and miRNA sequencing. We found that PCC/PGL are characterized by a low mutation rate, with few recurrent somatic mutations and focal copy number alterations (CNAs). In contrast, we detected recurrent broad CNAs strongly associated with known molecular groups, often leading to the biallelic inactivation of the known susceptibility genes of PCC/PGL. We also identified DNA methylation changes and miRNA expression clusters strongly associated with molecular groups. Of note, overexpression of the miRNA cluster 182/96/183 is specific of SDHB-mutated tumors and induces invasive traits, whereas silencing of the imprinted DLK1-MEG3 miRNA cluster due to a loss of heterozygosity of the 14q32.2 locus is a potential driver in a subset of sporadic tumors. This comprehensive analysis illustrates the functional interdependence between genomic and epigenomic dysregulations underlying PCC/PGL.

2015-02-02 | E-MTAB-2833 | biostudies-arrayexpress

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Project description:Purpose: Identification of miRNA expression profiles of selected horse tissues. Methods: miRNA-seq analysis was performed on lung, heart and liver samples collected from 4 horses. The miRNA libraries were constructed from total RNA using NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs) according to the manufacturer protocol. The quantification of the obtained libraries was performed on a Qubit 2.0 spectrophotometer (Invitrogen, Life Technologies), while a quality control on a TapeStation 2200 instrument (D1000 ScreenTape; Agilent). 75 single-end cycle sequencing was performed on the NextSeq 500/550 platform (Illumina) with the use of NextSeq High Output Reagents v2 (Illumina). Results: The comparison of miRNA profiles between the investigated tissues revealed 185 differentially expressed microRNAs (p adj≤0.05) in the heart samples versus the liver samples, 172 DE miRNAs (p adj ≤0.05) in the lung samples in comparison to the liver samples, and 155 in the lung samples versus the heart samples. Conclusions: Obtained results show varied miRNA expression profiles characteristics for each investigated hore tissue.

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2022-11-28 | GSE148900 | GEO

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