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Sample GSM1387949 Query DataSets for GSM1387949
Status Public on Jun 01, 2015
Title RNA Seq Dnmt3L KO 20dpp
Sample type SRA
Source name Dnmt3L_KO_20dpp_testis
Organism Mus musculus
Characteristics strain background: C57BL/6
genotype/variation: Dnmt3L knockout
age: post-natal day 20
tissue: testis
Extracted molecule total RNA
Extraction protocol TRIZOL
Illumina TruSeq Stranded mRNA LT
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
Data processing Illumina Casava1.8.2 software used for basecalling.
RNA-seq libraries were first depleted of reads coming from rRNA by subtracting those reads that map to rRNA sequences (GenBank identifiers: 18S NR_003278.3, 28S NR_003279.1, 5S D14832.1, 5.8S K01367.1) with Bowtie
The rRNA depleted libraries were then mapped on the Mouse reference genome (mm9) using the Bowtie software allowing zero mismatch and 10 000 best alignments per read.
Reads were annotated using the RepeatMasker database and were weighted by the number of mapping sites.
Genome_build: mm9
Supplementary_files_format_and_content: Text files with the quantification of repeated elements.
Submission date May 16, 2014
Last update date May 15, 2019
Contact name Nicolas Servant
Organization name Institut Curie
Street address 26 rue d'ulm
City Paris Cedex 05
ZIP/Postal code 75248
Country France
Platform ID GPL17021
Series (2)
GSE57745 Transposon expression kinetics in Dnmt3L-/- developing testes [RNA-seq]
GSE57747 Kinetics of transposon-derived transcripts and piRNAs in the absence of DNA methylation during mouse spermatogenesis
BioSample SAMN02782231
SRA SRX545705

Supplementary file Size Download File type/resource
GSM1387949_D3L_KO_20dpp_RNA.txt.gz 9.5 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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