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| Status |
Public on Jul 02, 2019 |
| Title |
RNA m5C analysis in human urothelial carcinoma of the bladder (UCB) and adjacent normal tissues. |
| Organism |
Homo sapiens |
| Experiment type |
Methylation profiling by high throughput sequencing
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| Summary |
36 cases of UCB and 29 adjacent normal bladder tissues (22 pairs) were derived from patients diagnosed with UCB and received radial cystectomy at Sun Yat-sen University Cancer Center (SYSUCC, Guangzhou, China).Total RNA was isolated using TRIzol® Reagent (Ambion). The RNA concentration and quality were determined with NanoDrop, Qubit and agarose gel analysis. The Dynabeads® mRNA Purification Kit (Ambion) was used to enrich the mRNAs, which were used as templates for RNA-BisSeq library construction. For RNA-BisSeq, bisulfite-treated mRNAs were first subjected to reverse transcription with ACT hexamers and Superscript II Reverse Transcriptase (Invitrogen), and the following processes were carried out with KAPA mRNA Stranded mRNA-Seq Kit (KAPA) according to the manufacturer’s instructions. The libraries were sequenced on the Illumina HiSeq X-Ten platform at Novogene (Tianjin, CA) with paired-end 150 bp read length. The m5C sites were called using meRanCall from meRanTK (FDR < 0.01). The differential m5C sites were detected and the hypermethylated m5C in UCB samples correlates with oncogene mRNA overexpression in UCBs.
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| Overall design |
Examination of RNA m5C changes in UCB patients
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| Contributor(s) |
Chen X, Li A, Sun B, Xie D, Yang Y |
| Citation(s) |
31358969 |
| Submission date |
Jul 01, 2019 |
| Last update date |
Apr 23, 2020 |
| Contact name |
Bao-Fa Sun |
| E-mail(s) |
sunbf@big.ac.cn
|
| Organization name |
Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)
|
| Street address |
Da-Tun Road
|
| City |
Beijing |
| ZIP/Postal code |
100101 |
| Country |
China |
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| Platforms (1) |
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| Samples (65)
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| This SubSeries is part of SuperSeries: |
| GSE133671 |
m5C Promotes Pathogenesis of the Bladder Cancer Through Stabilizing mRNAs |
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| Relations |
| BioProject |
PRJNA552054 |
| SRA |
SRP212700 |
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