|
| Status |
Public on Apr 02, 2018 |
| Title |
input_ChIPseq_forebrain E14.5_WT |
| Sample type |
SRA |
| |
|
| Source name |
fetal forebrain E14.5
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
time point: no treatment
chip antibody: none
|
| Treatment protocol |
Mice did not recieve any treatment
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
After dissection, cells were cross-linked by 5 min of 1% formaldehyde treatment at 37˚C. The chromatin was sonicated using Bioruptor UCD-250. After IP, stringent washes, reverse cross-linked and proteinase K treatment, DNA was extracted using PCR purification kit (QIAGEN).
ChIP-seq library were prepared with ChIP-seq sample prep kit (illumina) for the paired end read Illumina HiSeq 2000 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 (PubMed ID: 18798982) and extended fragment pileup was saved into wig format.
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated using MACS2
|
| |
|
| 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) |
| 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 |
SAMN07503261 |
| SRA |
SRX3091725 |
