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Sample GSM2750487 Query DataSets for GSM2750487
Status Public on Apr 02, 2018
Title H3K9me3_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: H3K9me3 (ab8898)
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 SAMN07534147
SRA SRX3110382

Supplementary file Size Download File type/resource
GSM2750487_MEF_H3K9m3_subtract_wt.bw 617.9 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

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