|
| Status |
Public on Aug 04, 2017 |
| Title |
Cancer 2 |
| Sample type |
SRA |
| |
|
| Source name |
bladder cancer tissue
|
| Organism |
Homo sapiens |
| Characteristics |
tumor stage: T3N0M0
age(years): 70
gender: male
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The total RNA samples of three pairs of bladder cancer and normal bladder tissues were treated with the RiboZero rRNA Removal Kit and RNase R for deleting rRNA and linear RNA, according to the manufacturer’s instructions.
The rRNA depleted and RNase R digested RNA samples were fragmented and synthesized cDNA with random primer. Purified the PCR amplification products of cDNA, then the libraries were quality controlled and sequenced by HiSeq2000 (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
circRNA_expression.xls header = zhangyuanpingT
|
| Data processing |
Illumina Casava 1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Seqtk and Perl version 5.8.8
Sequenced reads were aligned to the hg38 genome assembly using BWA version 0.7.10 with parameters: -t 8 -k 19
CircRNA predicted and junction reads measurements were analysed using CIRI version 1.2 with parameters: -P --high-strigency
Differential expression were analysed using edgeR function package in R program version 3.10.0
Genome_build: ensembl hg38
Supplementary_files_format_and_content: tab-delimited text files include normalized SRPBM values and raw fragment counts for each Sample
|
| |
|
| Submission date |
Mar 30, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Yawei Li |
| E-mail(s) |
lyw2138@163.com
|
| Organization name |
Union Hospital, Tongji Medical College, Huazhong University of Science and Technology
|
| Street address |
Jiefang road
|
| City |
Wuhan |
| State/province |
Hubei |
| ZIP/Postal code |
430002 |
| Country |
China |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE97239 |
High-throughput RNA sequencing on circular RNA profiles of human bladder cancer tissues and normal bladder tissues |
|
| Relations |
| BioSample |
SAMN06667822 |
| SRA |
SRX2693001 |
