|
| Status |
Public on Jun 03, 2014 |
| Title |
WT_RNASeq.rep2 |
| Sample type |
SRA |
| |
|
| Source name |
mouse embryonic stem cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: mouse embryonic stem cells
genotype: Dnmt3a/3b DKO
|
| Growth protocol |
mESCs were grown in DMEM supplemented with 15% FBS (HyClone), 20 mM Hepes, 0.1 mM nonessential amino acids, 0.1 mM 2-mercaptoethanol, 100 U/mL penicillin, 0.05 mM streptomycin, leukemia inhibitory factor (1000 U/ml), and 2 mM glutamine.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol (Invitrogen) according to manufacturer's instruction. Ribosomal RNA was removed using RiboMinus Eukatyote Kit (Invitrogen).
The mRNA libraries were prepared for strand-specific sequencing as described previously (Parkhomchuk et al. 2009).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.4
RNA-seq reads trimmed to 36bp length and were aligned to the mm9 genome assembly using TopHat giving rise to bam files
BigWig files were created based on TopHat output, as Bam files were used to calculate read density file using the genomeCoverage script from the Bedtools suite. For comparability, read density numbers were normalized by a factor based on total number of reads per sample
Genome_build: mm9
|
| |
|
| Submission date |
Jun 12, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Ulrich Wagner |
| Organization name |
Uiversity Hospital Zurich
|
| Street address |
Schmelzbergstrasse 12
|
| City |
Zurich |
| ZIP/Postal code |
8091 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL11002 |
| Series (2) |
| GSE47883 |
Maintenance of DNA methylation in embryonic stem cells depends on the histone H3K9 methyltransferases (Dnmt3ab KO RNA-Seq) |
| GSE47894 |
Maintenance of DNA methylation in embryonic stem cells depends on the histone H3K9 methyltransferases |
|
| Relations |
| BioSample |
SAMN02202307 |
| SRA |
SRX304998 |
