NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2739378 Query DataSets for GSM2739378
Status Public on Apr 02, 2018
Title H3K9me3_ChIPseq_forebrain E14.5_WT1
Sample type SRA
 
Source name fetal forebrain E14.5
Organism Mus musculus
Characteristics strain: C57BL/6
time point: no treatment
chip antibody: H3K9me3 (MABI0308)
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 SAMN07503264
SRA SRX3091723

Supplementary file Size Download File type/resource
GSM2739378_H3K9me3_L2toL1_treat_pileup.bw 486.6 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap