|
| Status |
Public on Apr 02, 2018 |
| Title |
RNAseq_Setdb1 cKO iMEFs_4OHT_siDnmt1_1 |
| Sample type |
SRA |
| |
|
| Source name |
iMEF
|
| Organism |
Mus musculus |
| Characteristics |
cell type: iMEF (Setdb1 cKO iMEF)
treatments: day 6 after 4OHT treatment with Dnmt1 siRNA
|
| Treatment protocol |
For knockdown, siRNAs targeting Dnmt1 or control siRNA was transfected into Setdb1 cKO iMEFs using RNAiMAX. Transfected cells were passaged 24 h after transfection. A second transfection was conducted with the same reagents on the following day. Cells were harvested at day 6 and RNA was isolated. For simultaneous KO of Setdb1, 4OHT was added at day 0.
|
| 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).
RNA libraries were prepared for sequencing using Illumina TruSeq RNA Sample Prep Kit protocols
|
| |
|
| 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 the exception of “-g 1”.
Mm9 Refseq gtf file was downloaded from UCSC (http://genome.ucsc.edu) in Oct 22, 2014 and applied as gene annotation file.
After obtaining the aligned bam files, the Cufflinks algorithm was used to calculate FPKM with the Refseq gtf file.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
|
| |
|
| Submission date |
Aug 22, 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 |
SAMN07535870 |
| SRA |
SRX3110380 |
