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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jun 10, 2015 |
| Title |
Somatic piRNAs in the adult mouse |
| Organism |
Mus musculus |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
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| Summary |
Small RNAs were deep sequenced from the liver and spleen of adult mice in an effort to identify somatic piRNAs. Following sequencing of all small RNAs, known non-coding RNAs were computationally removed from the dataset. The remaining RNAs were then mapped to the genome and analyzed for sequence characteristics (5' base, length) typical of known piRNAs. To determine if any of the identified small RNAs were MIWI2 dependent, we deep sequenced small RNAs from liver and spleen of MIWI2 KO mice and analyzed them as above.
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| Overall design |
We deep sequenced small RNAs from the liver and spleen of one WT mouse and one MIWI2 knock-out mouse. We then trimmed sequencing adapters and removed known ncRNAs (rRNA, tRNA, snoRNA, snRNA, miRNA) from the dataset before aligning reads to the mm9 assembly of the mouse genome.
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| Contributor(s) |
Yamtich J, Heo S, Dhahbi J, Martin D, Boffelli D |
| Citation(s) |
26076733 |
| Submission date |
May 20, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Dario Boffelli |
| E-mail(s) |
dario.boffelli@cshs.org
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| Organization name |
Cedars Sinai
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| Department |
Pediatrics
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| Lab |
Boffelli
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| Street address |
700 N San Vicente Blvd
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| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90069 |
| Country |
USA |
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| Platforms (1) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
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| Samples (4)
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| Relations |
| BioProject |
PRJNA203543 |
| SRA |
SRP022904 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE47093_RAW.tar |
80.0 Kb |
(http)(custom) |
TAR (of BED, TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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