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Series GSE47093 Query DataSets for GSE47093
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
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.
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.
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
Organization name Cedars Sinai
Department Pediatrics
Lab Boffelli
Street address 700 N San Vicente Blvd
City Los Angeles
State/province CA
ZIP/Postal code 90069
Country USA
Platforms (1)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (4)
GSM1144684 Liver
GSM1144685 Spleen
GSM1144686 LiverMiwi2KO
BioProject PRJNA203543
SRA SRP022904

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Supplementary file Size Download File type/resource
GSE47093_RAW.tar 80.0 Kb (http)(custom) TAR (of BED, TXT)
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Raw data are available in SRA
Processed data provided as supplementary file

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