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High-throughput RNA sequencing on circular RNA profiles of human triple-negative breast cancer and adjacent normal tissues

ABSTRACT: High-throughput RNA sequencing on circular RNA profiles of human triple-negative breast cancer and adjacent normal tissues

PROVIDER: PRJNA450481 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7012370_1.fastq.gz	Fastqsanger.gz
	SRR7012370_2.fastq.gz	Fastqsanger.gz
	SRR7012371_1.fastq.gz	Fastqsanger.gz
	SRR7012371_2.fastq.gz	Fastqsanger.gz
	SRR7012366_1.fastq.gz	Fastqsanger.gz

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High-throughput RNA sequencing on circular RNA profiles of human triple-negative breast cancer and adjacent normal tissues

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.

2018-12-06 | GSE113230 | GEO

Circular RNA (circRNA) expression profiles in hypopharyngeal carcinoma tissues vs. adjacent normal mucosae detected by microarray

Project description:Circular RNA (circRNA) expression profiles in hypopharyngeal carcinoma tissues vs. adjacent normal mucosae detected by microarray

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Profiling of circular RNAs in gastric cancer tissues and adjacent normal tissues

Project description:Profiling of circular RNAs in gastric cancer tissues and adjacent normal tissues

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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.

2022-03-15 | GSE193453 | GEO

High-throughput RNA sequencing on circular RNA profiles of human bladder cancer tissues and normal bladder tissues

Project description:In order to find out circular RNAs profiles in human bladder cancer tissues and normal bladder tissues, we characterized circuclar RNA transcripts by performing RNA-Seq on ribosomal RNA-depleted total RNA from three pairs of human bladder cancer tissues and paired normal bladder tissues.A computational pipeline based on the anchor alignment of unmapped reads was used to identify circular RNAs. Collectively, we identified16,535 distict circular RNAs, most of them origined from exons (88.96%), others from introns, linc RNA, intergenic region, 3’UTR and 5’UTR. Among all these circRNAs, 571 circRNAs were differentially expressed between bladder cancer tissues and normal bladder tissues, and 524 circRNAs were downregulated in bladder cancer tissues (91.2%), others were upreguluated. These significantly differential expressed circular RNA might have regulatory function in bladder cancer, and worth to be further explored.

2017-08-04 | GSE97239 | GEO

RNA-sequencing: HNSCC tissue and adjacent normal tissue

Project description:RNA-sequencing: HNSCC tissue and adjacent normal tissue

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A Circular RNA Controls Ribosomal RNA Maturation and Atherosclerosis in Humans

Project description:Circular RNAs (circRNAs) are broadly expressed in eukaryotic cells, but their role in human health and disease remains obscure. Here, we show that circular antisense non-coding RNA in the INK4 locus (circANRIL), which is transcribed at a locus of atherosclerotic cardiovascular disease on chromosome 9p21, confers athero-protection by controlling ribosomal RNA (rRNA) maturation and modulating pathways of atherogenesis. At the molecular level, circANRIL competes with precursor rRNA (pre-rRNA) for binding to pescadillo homolog 1 (PES1), an essential 60S-preribosomal assembly factor, thereby impairing exonuclease-mediated pre-rRNA processing and ribosome biogenesis. As a consequence, circANRIL induces nucleolar stress and p53 activation, resulting in the induction of apoptosis and inhibition of proliferation, which are key athero-protective cell functions within the arterial wall. Collectively, these findings identify circANRIL as a prototype of a circRNA regulating ribosome biogenesis and conferring athero-protection, thereby unveiling a therapeutic potential of certain circRNAs in human disease.

2017-03-28 | MSV000080698 | MassIVE

A Circular RNA Controls Ribosomal RNA Maturation and Atherosclerosis in Humans

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Profiling of circular RNAs in gastric cancer tissues and adjacent normal tissues

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.

2019-11-01 | GSE121445 | GEO

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