|
| Status |
Public on Jun 01, 2015 |
| Title |
RNA Seq Dnmt3L KO 16.5dpc |
| Sample type |
SRA |
| |
|
| Source name |
Dnmt3L_KO_16.5dpc_testis
|
| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL/6
genotype/variation: Dnmt3L knockout
age: pre-natal day 16.5
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 |
| E-mail(s) |
Nicolas.Servant@curie.fr
|
| 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 |
|
| Relations |
| BioSample |
SAMN02782228 |
| SRA |
SRX545701 |
