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Profiling of mRNAs, long chain non-coding RNAs and circular RNAs in gastric cancer tissues and adjacent normal tissues

ABSTRACT: Profiling of mRNAs, long chain non-coding RNAs and circular RNAs in gastric cancer tissues and adjacent normal tissues

PROVIDER: PRJNA796293 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR17551600.fastq.gz	Fastqsanger.gz
	SRR17551601.fastq.gz	Fastqsanger.gz
	SRR17551590_1.fastq.gz	Fastqsanger.gz
	SRR17551590_2.fastq.gz	Fastqsanger.gz
	SRR17551591_1.fastq.gz	Fastqsanger.gz

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Profiling of mRNAs, long chain non-coding RNAs and circular RNAs in gastric cancer tissues and adjacent normal tissues

Project description:Purpose: To investigate the role and mechanism of mRNAs, long chain non-coding RNAs and circular RNAs in gastric cancer. Methods: RNA-seq of ribosomal RNA-depleted total RNA were performed to screen differential expressed mRNAs, long chain non-coding RNAs between paired gastric cancer tissues and adjacent normal tissues.For the linear RNA was digested with 3 U of RNase R per µg of RNA. Results: A total of 83672 mRNAs, 105998 long chain non-coding RNAs, 25441 distinct circRNAs were identified in these samples, and 13929 of these circRNAs were identified as novel circRNAs.

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Project description:In an attempt to search for metastasis-associated circRNAs, we performed RNA-sequencing on ribosomal RNA-depleted total RNA from three pairs of triple-negative breast cancer (TNBC) and adjacent normal tissues. A computational pipeline based on the anchor alignment of unmapped reads was used to identify circular RNAs. Taken together, 69,815 distinct circRNAs were found in this study and 87% were derived from exons, and the others were derived from introns, intergenic region and 3′ or 5′ UTR, etc. We further identified 5,033 differentially expressed circRNAs (fold change ≥ 2 and p < 0.05). Among them, 3,726 circRNAs were significantly down-regulated and 1,307 circRNAs were significantly up-regulated in TNBC tissues compared with adjacent normal tissues. These data indicate that circRNAs are abundant in human breast tissues and dysregulation of circRNAs may contribute to breast cancer progression.

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Project description:Purpose: To investigate the role and mechanism of circRNAs in gastric cancer. Methods: RNA-seq of ribosomal RNA-depleted total RNA and qRT-PCR were performed to screen differential expressed circRNAs between paired gastric cancer tissues and adjacent normal tissues. Results: A total of 57623 distinct circRNAs were identified in these samples, and 35120 of these circRNAs contained at least two independent back-spliced reads in at least two samples. Compared with circBase, we found that there were 29007 matched circRNAs and 28616 novel circRNAs in our study.

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Circular DNA tumor viruses make circular RNAs

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