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Sample GSM475281 Query DataSets for GSM475281
Status Public on Jan 04, 2010
Title total RNA
Sample type SRA
 
Source name total RNA
Organism Mus musculus
Characteristics stage: adult
size selection: ~18-30 nt
antibody: none
Treatment protocol Testes extract was produced by decapsulating testicles, washing and resuspending spermatogenic tubules in protein extraction buffer, then douncing tubules with 20 strokes of a Type B glass pestle. Extract was then cleared with a 30 minute, 10,000 g spin, and snap frozen.
Growth protocol Mouse testes were dissected from euthanized adult male swiss webster mice.
Extracted molecule total RNA
Extraction protocol The anti-Mili or anti-Miwi antibody was immobilized onto magnetic beads, and beads were suspended in testes extract for 1 hour. Retained beads were washed 6 times with 1X PBS, then total RNA from the IP was extracted with Tri-reagent. Total RNA from whole testes extract was also extracted with Tri-reagent. Adapters were ligated to the small RNA component from the IP or total RNA, and a cDNA library was produced by reverse-transcription of the adapter-ligated small RNAs. The cDNA library was gel purified, quantitated, and coupled to a flow cell for sequencing on the Illumina Genome Analyzer II.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina Genome Analyzer II
 
Description total RNA
IP and gel-purification, RNA-seq.
Sequencing of small RNAs from Mili IP, Miwi IP, and total RNA from mouse adult testes extract.
Data processing Raw sequences were clipped by 3' linker sequences recognition, and clipped sequences longer than 18 nt were selected for analysis.
The processed data files (*seq ) are the result of the pipeline: Raw files -> remove the linker sequences -> count the number of each sequence.
 
Submission date Nov 24, 2009
Last update date May 15, 2019
Contact name Nicolas Robine
E-mail(s) robinen@mskcc.org
Organization name Memorial Sloan Kettering Cancer Center
Department Developmental Biology
Lab Eric Lai
Street address 1275 York Avenue, Box 252
City New York
State/province NY
ZIP/Postal code 10065
Country USA
 
Platform ID GPL9250
Series (1)
GSE19172 Mili-IP, Miwi-IP, and total RNA from mouse adult testis
Relations
SRA SRX015662
BioSample SAMN00007437

Data table header descriptions
SEQUENCE
COUNT # of reads

Data table
SEQUENCE COUNT
TTGTAAAGAGTGTGATGACTGAGTGACGGGCGTATT 1
TGGTAGTACCCGGTGAAGACAAAATCATTT 1
TTCAGTGATGATTAGCTTCTGACTTT 1
TACTACATATGTGCCCCTGCACGCTTGAGTCGTATG 1
TAGGAGCTTGGCAAACAGTGACTGGCTAGGTCGTAT 1
GACTGTTCCCGTCTCCCTCCAAAC 1
CAAAGCAACTATGTTGATGGTATGGATTC 1
TTTCTCACTCTGCAGACTTTCTGAGTTGGT 1
ATTGAAGCCAAGTGCATATATTAAGA 1
CTTTACAAATGAGGAGGCTGGCAGCTG 1
GACATGACGAGAAGAGGGCGAATCTCTAGT 2
TCCCAAGCTTCTGGTGATCTCTCAATGC 1
TATCATTGGGCCAGATGGGCA 1
TAATGTAAAATGGTCACTGGAGGGGA 2
CACAGGGCTTATGGCCTTCCATGGCTGTGGTATGT 1
AACTGAAAGCATGGGACC 1
CTTCTCAGCTGGCACCTTGTACATGGTT 1
TATAGCCAGAGTACAGAGA 1
GAAGGGCAACTACATCCGGATGGCGT 1
TCATAGCCAAAAAGCTGAGAAGCAACGAGG 1

Total number of rows: 2742326

Table truncated, full table size 84986 Kbytes.




Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA

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