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Sample GSM2059183 Query DataSets for GSM2059183
Status Public on May 08, 2016
Title Np95 wt ESC [ChIP-seq]
Sample type SRA
Source name ES cells
Organism Mus musculus
Characteristics strain background: C57BL/6
cell type: embryonic stem cells (ESCs)
genotype/variation: Np95 (flox/flox) conditional alleles; CreERT2 transgene
treated with: Without 4-OHT (day 0)
chip antibody: Anti-H3K9me3 mAb (MBL, MABI0318)
molecule subtype: Crosslinked chromatin
Growth protocol Standard condition for ES cells.
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was isolated using QIAGEN All-prep kit
Libraries were prepared according to NEB's instructions accompanying the NEBNext® ChIP-seq Library Prep Reagent set for Illumina. Adapter ligated DNA was PCR amplified with Illumina primers for 15 cycles. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Hi-Seq 1000 following the manufacturer's protocols.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 1500
Description ESCs were corsslinked with 1% formaldehyde and after nuclear lysis, chromatin was sheared by sonication (30s on/off, 15 cycles) and immunoprecipitated with an anti-H3K9me3 antibody (MBL, MABI0318) using Protein A + G magnetic beads (Millipore)
Data processing Basecalls performed using Illumina offline basecaller (OLB) version 1.9.4
ChIP-seq sequences were aligned on mm9 using bowtie2 (version 2.1.0) with default parameters.
Accumlated reads were mapped on mouse genome and reads per kilobase is recorded in processed files.
Genome_build: mm9
Supplementary_files_format_and_content: Whole genome mapped read counts normalized by the total mapped reads and genome size (mapped reads per kilobase genome per million reads). Mapped reads per kilobase
Submission date Feb 10, 2016
Last update date May 15, 2019
Contact name Takaho A. Endo
Organization name RIKEN
Department IMS
Lab Laboratory for Integrative Genomics
Street address 1-7-22 Suehiro, Tsurumi
City Yokohama
State/province Kanagawa
ZIP/Postal code 230-0045
Country Japan
Platform ID GPL18480
Series (2)
GSE77779 Protracted NP95 binding to hemimethylated DNA disrupts SETDB1-mediated proviral silencing [ChIP-seq]
GSE77781 Protracted NP95 binding to hemimethylated DNA disrupts SETDB1-mediated proviral silencing
BioSample SAMN04485142
SRA SRX1569975

Supplementary file Size Download File type/resource
GSM2059183_S02263.wig.gz 1.7 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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