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| Status |
Public on Sep 01, 2013 |
| Title |
Testicular_cancer_06_N_miRNA |
| Sample type |
SRA |
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| Source name |
testicular, normal
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| Organism |
Homo sapiens |
| Characteristics |
cell type: testicular germ
cancer or normal: normal
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| Extracted molecule |
total RNA |
| Extraction protocol |
5μg of total RNA extracted from each sample was ligated with both 5âadapter and 3âadapter for reverse transcription by Superscript II, and the reverse transcribed products were amplified subsequently. After collection of ~92bp DNA band on the 6% PAGE gels, PCR products were ethanol precipitated and purified by Spin-X filter columns. Finally, miRNA libraries were sequenced on the Illumina Cluster Station and Genome Analyzer â
¡ sequence system following the manufacturerâs protocol.
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| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer II |
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| Description |
T27N
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| Data processing |
Low quality reads were trimmed and adapter sequences were accurately clipped with the aid of a dynamic programming algorithm before subsequent statistical analysis. After elimination of the duplicated reads, the remaining reads no shorter than 18nt were mapped to human reference genome (hg18) using SOAP V2.0. To remove tags originating from protein coding genes, repeat sequences, rRNA, tRNA, snRNA, and snoRNA, we also mapped the short read tags to UCSC RefGene, RepeatMasker and NCBI Refseq, as well as our in-house ncRNA annotation data sets compiled from the NCBI Genbank database (http://www.ncbi.nih.gov). The similar pipeline used for DGE mRNA differential expression analysis was also applied to miRNAs study. We investigated the biological relevance of miRNA through their regulation of target genes. First, pearson correlation analysis was perform to identify potential targets. Meanwhile, another target gene set was generated according to the intersect result of any two predicted algorithms of DIANA-microT 3.0, TargetScan 5.1, and PicTar. Next, those potential targets defined by the predicted target gene set above were subjected to further analysis.
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| Submission date |
Aug 23, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Jiahao Chen |
| E-mail(s) |
chenjiahao@genomics.org.cn
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| Organization name |
Beijing Genomics Institute
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| Department |
Cancer Research Group
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| Street address |
Beishan road, Yantian district
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| City |
Shenzhen |
| State/province |
Guangdong |
| ZIP/Postal code |
518083 |
| Country |
China |
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| Platform ID |
GPL9115 |
| Series (2) |
| GSE31616 |
microRNA expression of cancer and matched adjacent tissues from 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 |
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| Relations |
| SRA |
SRX093220 |
| BioSample |
SAMN00714148 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM785440_T27N_match_hairpin_aln.txt.gz |
133.0 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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