|
| Status |
Public on Apr 02, 2018 |
| Title |
RNAseq_Setdb1 KO iMEFs_long_2 |
| Sample type |
SRA |
| |
|
| Source name |
iMEF
|
| Organism |
Mus musculus |
| Characteristics |
cell type: iMEF (Setdb1 cKO iMEF)
time point: more than 2weeks after 4OHT treatment
|
| Treatment protocol |
For KO 4OHT was treated for first 4days then cells were harvested at day 5
|
| Growth protocol |
Cells were cultured in DMEM (Nacalai: 08458-45) with MEM non-essential amino acids (Gibco: 11140-035), 2-mercaptoethanol (used at 0.1 mM, Nacalai), 10% FBS. Cells were split every three days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with RNeasy mini kit (QIAGEN: 74134).
rRNA was removed using epicentre's Ribo-Zero rRNA Removal kit. Illumina TruSeq RNA Sample Prep Kit was used for the construction of sequencing libraries.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Data processing |
We aligned reads to the reference genome (UCSC mm9) using TopHat (version 2.0.12 and 2.1.1) with "-g 1" parameter.
Mm9 Refseq gtf file was downloaded from UCSC (http://genome.ucsc.edu) in Oct 22, 2014 and applied as gene annotation file.
the Cufflinks algorithm was used to calculate FPKM with the Refseq gtf file, and two comparisons were done (WT vs cKO, WT vs cKO long culture)
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
|
| |
|
| Submission date |
Aug 10, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Masaki Kato |
| E-mail(s) |
mkato@riken.jp
|
| Organization name |
RIKEN
|
| Lab |
Cellular Memory Laboratory
|
| Street address |
2-1 Hirosawa
|
| City |
Wako |
| State/province |
Saitama |
| ZIP/Postal code |
3510198 |
| Country |
Japan |
| |
|
| Platform ID |
GPL18480 |
| Series (2) |
| GSE102486 |
A somatic role for the histone methyltransferase Setdb1 in endogenous retrovirus silencing [RNA-Seq] |
| GSE102490 |
A somatic role for the histone methyltransferase Setdb1 in endogenous retrovirus silencing |
|
| Relations |
| BioSample |
SAMN07503266 |
| SRA |
SRX3091721 |
