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Sample GSM545783 Query DataSets for GSM545783
Status Public on Jun 13, 2010
Title Mov10L1-associated piRNAs
Sample type SRA
 
Source name Testes
Organism Mus musculus
Characteristics strain: C57BL/6
genotype: wild type
age: Adult
antibody: Mov10l1 antibody (purified polyclonal)
Treatment protocol Testes were extracted from euthanized animals of indicated ages
Growth protocol Mice were maintained and genotyped as per standard procedures
Extracted molecule total RNA
Extraction protocol Mov10L1 was immunoprecipitated from mouse testes extracts, small RNAs recovered by phenol-choloroform extraction, 5'-end labelled with gamma-ATP and gel extracted.
Total RNA was separated by 15% Urea-PAGE and RNAs in the range of 18-32 nt were gel extracted. RNA libraries were prepared with Digital Gene Expression for Small RNA kit from Illumina.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina Genome Analyzer
 
Description Mov10l-associated small RNAs and total 18-32 nt small RNAs extracted after PAGE separation.
This sample represents Mov10L1 IP small RNAs.
Data processing In-house programs developed by Alexander Stark and Ravi Sachidanandam. Reads mapped to the genome (July 2007, mm9 assembly).
 
Submission date May 20, 2010
Last update date May 15, 2019
Contact name Ramesh Pillai
E-mail(s) ramesh.pillai@unige.ch
Organization name University of Geneva
Department Department of Molecular Biology
Street address 30, Quai Ernest-Ansermet
City Gneveva
ZIP/Postal code CH-1211
Country Switzerland
 
Platform ID GPL9185
Series (1)
GSE21763 Mouse MOV10L1 associates with Piwi proteins and is an essential component of the piRNA pathway
Relations
SRA SRX021364
BioSample SAMN00014096

Data table header descriptions
SEQUENCE
CHR
START
END
STRAND
COUNT readcount

Data table
SEQUENCE CHR START END STRAND COUNT
TGCAGGATTGAGACACTTCTGTTAGAAGAA chr1 4160439 4160468 - 1
TCGGAGAAGAGGTAGGAAGTGTGGC chr1 4774145 4774169 - 1
CAGTGGAAGACGGCAGCATTTTGGAGA chr1 4807590 4807616 + 1
ACTGGAGGAGAACGTTTATTTTAGAC chr1 4871856 4871881 + 2
ACTTCGTAGCTGTTCCGGCTTCCTCT chr1 5073205 5073230 + 1
CACTGAGACCTCGGAGCTCGACCGGCGC chr1 5073292 5073319 + 1
TGAGACCTCGGAGCTCGACCGGCGCC chr1 5073295 5073320 + 1
TAAAACATTTATAAATCTGATGACGCA chr1 5083449 5083475 + 1
TGCGAAACGAAGCAAGAGCACTGCCT chr1 5085731 5085756 + 1
TACCGGAATCTGCAATGCAAATGTGCTA chr1 5451827 5451854 - 1
TTACCGGAATCTGCAATGCAAATGTGCTA chr1 5451827 5451855 - 1
TACCGGAATCTGCAATGCAAATGTGCT chr1 5451828 5451854 - 1
AGGATGCATCTGTGTTACCTGATCTGTG chr1 6234913 6234940 + 1
ATATGAAATAGAAAAAAAACTGAAAGAAC chr1 6239922 6239950 + 1
AGAGTTATGTCGATGGGAATATACAG chr1 6240634 6240659 + 1
TGTGAGGAATTTTTTGTGAGACGACCG chr1 6241668 6241694 + 1
TGAGGAATTTTTTGTGAGACGACCGGC chr1 6241670 6241696 + 1
TGAGACGACCGGCTACAACCACTTCT chr1 6241684 6241709 + 1
ACAACCACTTCTGGAGAATAGGACGG chr1 6241698 6241723 + 1
ACCACTTCTGGAGAATAGGACGG chr1 6241701 6241723 + 1

Total number of rows: 387977

Table truncated, full table size 21012 Kbytes.




Supplementary data files not provided
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Processed data included within Sample table
Raw data are available in SRA
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