|
Status |
Public on May 20, 2020 |
Title |
RNA-seq_DKO_Rep5 |
Sample type |
SRA |
|
|
Source name |
RNA-seq_DKO_E8.5 whole embryos
|
Organism |
Mus musculus |
Characteristics |
strain background: C57BL/6J genotype/variation: Dnmt3a-/- Dnmt3b-/- developmental stage: E8.5 gender: Male tissue/cell type: whole embryos
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was extracted with the AllPrep DNA/RNA Mini Kit (Qiagen). RNA-Seq libraries were prepared with the TruSeq Stranded Total RNA Sample Prep Kit (Illumina) with Ribo-Zero depletion according to the manufacturer’s instructions.
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 4000 |
|
|
Data processing |
Reads were aligned to the mouse mm10 genome with TopHat2 v2.0.13 using default parameters and a RefSeq transcriptome index.
For data visualization, bigwig files were generated using bam2wig.py from the RSeQC package v2.6.4 using the parameters -u -t 5000000000.
Genome_build: mm10
Supplementary_files_format_and_content: BigWig files for RNA-seq visualization.
|
|
|
Submission date |
May 06, 2019 |
Last update date |
May 20, 2020 |
Contact name |
Michael Weber |
Organization name |
CNRS
|
Department |
UMR7242 Biotechnology and Cell Signalling
|
Street address |
300 Bd Sebastien Brant
|
City |
Illkirch |
ZIP/Postal code |
67412 |
Country |
France |
|
|
Platform ID |
GPL21103 |
Series (1) |
GSE130735 |
Genome-wide roles of DNA methyltransferases in mouse embryos |
|
Relations |
BioSample |
SAMN11580859 |
SRA |
SRX5795128 |