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Sample GSM822762 Query DataSets for GSM822762
Status Public on Nov 30, 2011
Title Testes, Adult Miwi -/ADH [MR25]
Sample type SRA
 
Source name Testes, Adult Miwi -/ADH
Organism Mus musculus
Characteristics developmental stage: Adult
tissue: Testes
strain: C57BL/6
genotype/variation: Miwi -/ADH
Growth protocol mice were mated, grown and kept under standard conditions
Extracted molecule total RNA
Extraction protocol Testes were dissected from male mice washed in and kept until processing in cold phosphate buffered saline solution.
Miwi-associated small RNAs were isolated from mouse testes and libraries prepared by sequential ligation of 5’- and 3’- RNA adapters. Sequencing was for 36 cycles using the Illumina Genome Analyzer IIx. For RNAseq of round spermatids total RNA was depleted of abundant RNAs like rRNAs using Ribo-Zero kit (Epicentre). Strand-specific RNAseq library was prepared using the ScriptSeq mRNA-seq Library Preparation Kit (Epicentre; Cat no. SS10906). Sequencing was for 76 cycles by the Illumina Genome Analyzer. For global 5’-RACE library, total RNA from purified round spermatids was depleted of rRNAs using the Ribo-Zero kit (Epicentre). Then Illumina 5’ RNA adapter was ligated to capture pre-existing 5’ ends. After purification using the Absolutely RNA kit (Stratagene), RNA was reverse-transcribed with a random primer and PCR amplified. PCR products of ~200 bp were gel-eluted for sequencing by the Illumina Genome Analyzer (105 cycles).
Most libraries are run in single lanes. Only one is duplexed and barcoded.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina Genome Analyzer IIx
 
Description Adult Library#1
Small RNA Miwi IP
Duplexed run: Reads with no barcode is MR25. Other library has barcode (CGAC)
read_length: 36
Data processing Barcodes where removed, and trimmed reads were mapped to the mouse genome mm9. The software used for processing the data (genomic coordinates etc) from the raw data files are in-house tools from Sachidanandam lab. They are described in a publication: Olson, A.J., Brennecke, J., Aravin, A.A., Hannon, G.J. & Sachidanandam, R. Analysis of large-scale sequencing of small RNAs. Pac Symp Biocomput, 126-36 (2008).
 
Submission date Oct 26, 2011
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 GPL11002
Series (2)
GSE32183 MIWI catalysis is required for piRNA amplification-independent LINE1 transposon silencing
GSE32184 MIWI catalysis is required for piRNA amplification-independent LINE1 transposon silencing [deep sequencing]
Relations
SRA SRX105275
BioSample SAMN00752497

Data table header descriptions
SEQUENCE
COUNT COUNT

Data table
SEQUENCE COUNT
ACCCAAAAGGACAUGUAUGGUAUGUACUC 0
UUUGGACUUAAAAGAAUGACCAGUGUCAA 0
CAGAAAGGAAAUAAUAGGCUUCUUGUUCC 0
UCUCAGGAUUUCUCUUCAGCACUUUCCC 0
GAAGCUGGAAAGAAAGAACAACUGGGAAAU 0
AAAGAGAGAAUACAAGGAGCUGGGUAC 1
UGGCCUGUGUGUGACAGUUUUGAUAUGGAG 0
UCUAAUGAAUAGUCAAAAUCUCUUUUUUAA 0
UAUGAAGGAUUGUUUUUUUAAAGGGCUGU 1
CACUAGGCUGUCUCUAAUGAUGUCAUGAGCAU 0
UGGUGCUAAGCAUGUAUCUUGAAAAGUGU 0
UUUGUAGAAUUUGAAAAGGAUAGGAUGC 0
UAGUUUUCAUGUAGAAGAGAAAAC 0
CCUAAAUUGAAGAAAAGGCUCAGGGCACUCGG 0
CCUAAAUACAUAUAUACAACCUGAUCGGUCUUU 1
AGGAGGUAGAUUAAAAUAUCAAGGAAG 5
UGGAAGAAAAGAGGAAAAUGGCAAAAGACA 0
AUGAUUGUUAAAGGAGGAAGCAUAGACU 0
UAUAUAUGUGAUAUGGUGAAGGUGGGA 6
UGGGAAUAAAAUGAUGUUGAUGUUGAAAC 16

Total number of rows: 17578027

Table truncated, full table size 684144 Kbytes.




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

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