|
| Status |
Public on Sep 01, 2013 |
| Title |
Testicular_cancer_01_C_mRNA |
| Sample type |
SRA |
| |
|
| Source name |
testicular, cancer
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: testicular germ
cancer or normal: cancer
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted from normal adjacent tissues and tumor tissues of 7 and 10 patients of testicular germ cell tumor (TGCT) and transitional cell carcinoma of bladder (TCC) respectively by TRIZOL reagent (Invitrogen, US) according to the manufactureâs protocol. The RNA integrity was evaluated by Agilent 2100 Bioanalyzer (Agilent Technologies, US).4μg total RNA extracted from each sample was used in digital gene expression (DGE) sequencing. In brief, reverse transcription reaction was performed after mRNA isolation using oligo(dT)18 beads. 5âadapter was ligated after NlaIII enzyme digestion, and subsequently 3âadapter was ligated after MmeI enzyme digestion. The PCR amplification of double-adapters flanked tags was run and the resulting ~85bp PCR products were ethanol precipitated and purified from the electrophoresis gels by Spin-X filter columns. Finally, mRNA libraries were sequenced on the Illumina Cluster Station and Genome Analyzer â
¡ (Illumina Inc, USA) sequence system following manufacturerâs protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
T3C
|
| Data processing |
Potentially erroneous tags (single copy tags and tags consisting of adaptor sequences or containing unknown sequences 'N') were filtered out. All 17 bp sequences next to the possible Nlaâ
¢ restriction sites in human reference genome (hg18) plus the 4 bp CATG restriction enzyme digested site were extracted and created as a new reference. Tags were mapped to the constructed reference using SOAP V2.0 allowing no more than one base mismatch. Only unique mapping tags were used for gene expression analysis. Standardized TPM (transcripts per million clean tags) values were applied for comparing gene expression between tumors and normal adjacent tissues. Expression fold change (tumor versus normal) for each gene was calculated as log2Ratio using TPM values. Next, we performed a rigorous significance test to determine the differentially expressed genes. The resulting P-values for all genes were corrected for multiple tests using FDR (False Discovery Rate) adjustment.
|
| |
|
| Submission date |
Aug 23, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Jiahao Chen |
| E-mail(s) |
chenjiahao@genomics.org.cn
|
| Organization name |
Beijing Genomics Institute
|
| Department |
Cancer Research Group
|
| Street address |
Beishan road, Yantian district
|
| City |
Shenzhen |
| State/province |
Guangdong |
| ZIP/Postal code |
518083 |
| Country |
China |
| |
|
| Platform ID |
GPL9115 |
| Series (2) |
| GSE31614 |
mRNA expression of cancer and matched adjacent tissues of 7 testicular germ cell tumors and 10 transitional cell carcinomas of bladder |
| GSE31617 |
Comparative mRNA and microRNA expression profiling of three genitourinary cancers reveals common hallmarks and cancer-specific molecular events |
|
| Relations |
| SRA |
SRX093255 |
| BioSample |
SAMN00714183 |
