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| Status |
Public on Mar 01, 2018 |
| Title |
Circular RNAs are super abundant in cervical tumor and plasma detected by high throughput microarray [RNA-Seq] |
| Organism |
Homo sapiens |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
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| Summary |
Circular RNAs (circRNAs) are a new class of endogenous and regulatory non-coding RNAs, but their expressions in tumor and plasma are largely unknown. Here, our study firstly suggested that microarray should be more efficient than RNA sequencing for circRNA profiling. Then, we detected ~80,000 circRNAs expressed in cervical tumors and matched normal tissues by microarray, and ~23,000 of them are differently expressed. The numbers of up- and down-regulated circRNAs during tumorigenesis are almost equal. In addition, we discovered that the expression of different circRNA isoforms from the same linear RNA also different. Strikingly, as much as ~18,000 circRNAs could be robustly detected in plasmas, and ~8,000 circRNAs show different expression after surgery of tumor removal. Altogether, taking advantage of the huge number of circRNAs detected in tumor and plasma, we provide strong evidence for circRNA expression, regulation and potential clinical application as non-invasive biomarkers.
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| Overall design |
The circRNA expression in Universal Human Reference RNA (UHRR, 2 replicated samples) was compared to circRNA expression in Ambion’s Human Brain Reference total RNA (HBRR, 2 replicated samples) from the Microarray Quality Control (MAQC) project; The circRNA expression in cervical tumor (10 samples) was compared to circRNA expression in adjacent normal tissue (control, 10 samples) of 10 patients; The mRNA expression in cervical tumor (10 samples) was compared to mRNA expression in adjacent normal tissue (control, 10 samples) of 10 patients; The circRNA expression in preoperative plasma samples (control,7 samples) was compared to circRNA expression in postoperative plasma samples (14 samples) of 8 out of 10 cervical cancer patients.Microarray based circRNA expression profiles were acquired using CapitalBio circRNA Human Gene Expression Microarray V1.0 screening for 87,935 distinct human circRNA candidates.
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| Contributor(s) |
Li S, Teng S, Wang D |
| Citation(s) |
29415187 |
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| Submission date |
Nov 29, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Shasha Li |
| E-mail(s) |
shashal@umich.edu
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| Phone |
01062798728
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| Organization name |
University of Michigan
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| Street address |
1109 Maiden Ln, ct apt 104
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| City |
ANN ARBOR |
| State/province |
MI |
| ZIP/Postal code |
48109 |
| Country |
USA |
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| Platforms (1) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
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| Samples (10)
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| This SubSeries is part of SuperSeries: |
| GSE90741 |
Circular RNAs are super abundant in cervical tumor and plasma detected by high throughput microarray |
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| Relations |
| BioProject |
PRJNA420201 |
| SRA |
SRP125806 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE107472_RAW.tar |
2.5 Mb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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