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Effect of USB1 depletion on global miRNome in human embryonic stem cells and K562

ABSTRACT: Effect of USB1 depletion on global miRNome in human embryonic stem cells and K562

PROVIDER: PRJNA931329 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR23335709.fastq.gz	Fastqsanger.gz
	SRR23335710.fastq.gz	Fastqsanger.gz
	SRR23335711.fastq.gz	Fastqsanger.gz
	SRR23335712.fastq.gz	Fastqsanger.gz
	SRR23335713.fastq.gz	Fastqsanger.gz

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Effect of USB1 depletion on global miRNome in human embryonic stem cells and K562

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Project description:The set of expressed microRNAs in a given cell type, or “miRNome”, can be explored under many different aspects. Many studies report modulations of the miRNome in a wide variety of cancers. Papillary thyroid cancer is the most prevalent type of endocrine cancer. The presence of nodal metastases increases the risk of recurrence and mortality. In our study, we performed microRNA deep sequencing (miRSeq) of 3 PTC, their matching normal tissues and nodal metastases and designed a new bioinformatic framework to analyze variations of the different aspects of the miRNome: expression profile, isomiRs and non-templated additions distributions, mutation or A-to-I RNA-editing. Furthermore, we validated our results using qRT-PCR on independent samples from 14 patients and using the collection of miRSeq data from The Cancer Genome Atlas (up to 495 miRseq of PTC). We gave a particular attention to cell content and contamination. We showed that microRNA expression profiles of thyrocytes are altered during tumorigenesis. These alterations involve known up regulations of microRNAs such as miR-146b-5p or miR-22-3p but also down regulations such as miR-7-5p, miR-7-2-5p, miR-1179 or miR-204-5p. Furthermore, some expression modulations were increased following the nodal metastatic process such as miR-7-2-3p or miR-138-1-3p. However, we did not find variations in the other aspects of the miRNome analyzed. We used our bioinformatic frameworks on the largest PTC miRSeq data collection available, to our knowledge. It allowed us, in one study on the different aspects of the miRNome, to find modulated microRNAs that could act as biomarkers of PTC.

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Effect of global or hypodermal depletion of RPOA-2

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Global transcriptional response to electron acceptors AKB and pyruvate in K562 cells

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