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| Status |
Public on Dec 01, 2015 |
| Title |
human epididymis |
| Sample type |
SRA |
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| Source name |
epididymis from a healthy and fertile man
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| Organism |
Homo sapiens |
| Characteristics |
gender: male
age: 26-year-old
tissue: epididymis
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| Treatment protocol |
The whole epididymis was immediately frozen in liquid nitrogen and stored at -80C for RNA extraction
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| Extracted molecule |
total RNA |
| Extraction protocol |
Briefly, total RNA was size-fractionated on a 15% (w/v) PAGE gel and then the 15-30 nt fraction was excised and purified with a 14-30nt ssRNA ladder (TaKaRa, Dalian, China) as molecular marker. After dephosphorylation by alkaline phosphatase, the small RNA was ligated sequentially to 5'- and 3'-adapters, followed by RT-PCR to produce the sequencing library. The PCR products were purified and sequenced with Solexa 1G Genome Analyzer (San Diego, USA).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
Sample 1
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| Data processing |
Sequence tags from the Solexa sequencing went through data cleaning, which included filtering out low quality tags and several contaminants. High quality reads were defined as no N (unknown nucleotide base) in the sequences, no more than 4 bases whose quality score was lower than 10 and no more than 6 bases whose quality score was lower than 13. The SOAP program was then used to map the small RNA tags to the genome. Thereafter all the tags were aligned with non-coding RNAs registered in GenBank (http://www.ncbi.nlm.nih.gov/) and Rfam (http://www.sanger.ac.uk/software/Rfam). After discarding the tags that matched rRNA (ribosomal RNA), tRNA (transfer RNA), repeat sequences, as well as mRNAs, the rest were searched for miRNAs in miRBase 17.0 (http://www.mirbase.org/index.shtml) and piRNAs (Piwi-interacting RNA) in Genebank by using programs developed by BGI. Mireap software developed by BGI was used to predict novel miRNA candidates on the basis of their secondary structure, the Dicer cleavage site and the minimum free energy of the un-annotated small RNA tags that could be mapped to the genome. The secondary structures were predicted by the MFOLD program [PMID:12824337].
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| Submission date |
Nov 28, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Yan Li |
| E-mail(s) |
liyan0535@yahoo.com.cn
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| Organization name |
Shandong Research Centre for Stem Cell Engineering
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| Street address |
20th, Yu Dong Road, Zhifu Area
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| City |
Yantai |
| State/province |
Shandong |
| ZIP/Postal code |
264000 |
| Country |
China |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE33966 |
Deep sequencing analysis of small non-coding RNAs reveals the diversity of microRNAs and piRNAs in the human epididymis. |
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| Relations |
| SRA |
SRX109243 |
| BioSample |
SAMN00760750 |
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