|
| Status |
Public on Dec 07, 2015 |
| Title |
MEF_DKO |
| Sample type |
SRA |
| |
|
| Source name |
Mouse embryonic fibroblasts
|
| Organism |
Mus musculus |
| Characteristics |
genotype/variation: TET1/TET2 knocked out
cell type: Mouse embryonic fibroblasts
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
RNA was extracted from frozen cell pellets using TRIzol (Invitrogen)
Sequencing libraries were prepared using 1µg of DNAse-treated total RNA in the first step of the TruSeq RNA Sample Preparation v2 protocol (Illumina, Part# 15026495 Rev. A) as recommended by the manufacturer.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
genomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Illumina Casava1.8.1 software used for basecalling.
Preprocessing, read trimming: shore 0.6.2
Preprocessing, quality filtering: shore 0.6.2
Transcriptome-mapping: tophat 2.0
Evaluation of differential expression: DESeq
Genome_build: mm9
Supplementary_files_format_and_content: Matrix-format created by DESeq containing the expression levels and p-values for differential expression
|
| |
|
| Submission date |
Jun 18, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Guenter Raddatz |
| Organization name |
German Center for Cancer Research
|
| Street address |
Im Neuenheimer Feld 580
|
| City |
Heidelberg |
| ZIP/Postal code |
69120 |
| Country |
Germany |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE58609 |
Tet1 and Tet2 mediate epigenetic regulation of developmental genes by protecting DNA methylation canyons against hypermethylation [RNA-Seq] |
| GSE58611 |
Tet1 and Tet2 mediate epigenetic regulation of developmental genes by protecting DNA methylation canyons against hypermethylation |
|
| Relations |
| BioSample |
SAMN02866174 |
| SRA |
SRX610349 |
