|
| Status |
Public on May 20, 2020 |
| Title |
RNA-seq_DKO_Rep2 |
| 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: Female
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 |
SAMN11580862 |
| SRA |
SRX5795125 |
