|
| Status |
Public on Apr 02, 2018 |
| Title |
input_ChIPseq_Setdb1 cKO iMEFs_WT |
| Sample type |
SRA |
| |
|
| Source name |
iMEF
|
| Organism |
Mus musculus |
| Characteristics |
cell type: iMEF (Setdb1 cKO iMEF)
time point: no treatment
chip antibody: none
|
| Treatment protocol |
For KO 4OHT was treated for first 4days then cells were harvested at day 7
|
| 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 |
genomic DNA |
| Extraction protocol |
The chromatin was digested with MNase. After IP, stringent washes, RNase and proteinase K treatment, DNA was extracted using PCR purification kit (QIAGEN). ChIP-seq library was prepared with KAPA hyperprep kit (KAPA biosystems) for the single read Illumina HiSeq 1500 platform.
ChIP-seq library were prepared with KAPA hyperprep kit (KAPA biosystems) for the single read Illumina HiSeq 1500 platform.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Data processing |
Sequence reads were mapped to the Mouse genome (mm9, July 2007) using BOWTIE2 (version 2.2.3). The default BOWTIE2 mapping of multi-hits reads to one of the possible genomic locations was used.
Peak-calling: Peak detection was performed with MACS2 (version 2.1.0.20140616) (PubMed ID: 18798982) and peaks were reported in BED format (q value< 0.005).
The DeepTools package (http://deeptools.github.io) was used to compute the differences between ChIP and Input samples. bigWig files were generated using bamCompare with option arguments “–normalizeUsingRPKM –ratio subtract –binSize 10”.
Genome_build: mm9
Supplementary_files_format_and_content: bed files were generated using MACS2. bigwig files were generated using DeepTools package
|
| |
|
| 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) |
| GSE102487 |
A somatic role for the histone methyltransferase Setdb1 in endogenous retrovirus silencing [ChIP-Seq] |
| GSE102490 |
A somatic role for the histone methyltransferase Setdb1 in endogenous retrovirus silencing |
|
| Relations |
| BioSample |
SAMN07534145 |
| SRA |
SRX3110384 |
