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Sample GSM2412764 Query DataSets for GSM2412764
Status Public on Nov 09, 2017
Title panCBFB_total
Sample type SRA
Source name Adult total thymocyte
Organism Mus musculus
Characteristics cell type: Adult total thymocyte
antibody: pan-Cbfb
Treatment protocol Cells were subjected to crosslinking and nuclei were lysed. Nuclei sample was sonicated using a model XL2000 ultrasonic cell disruptor (MICROSON). Sonicated chromatin was incubated overnight at 4 °C with magnetic beads-attached anti-Cbfb1, anti-Cbfb2, or pan-Cbfb polyclonal antibodies that were generated in our laboratory. Immunoprecipitated DNA was then purified.
Growth protocol Lineage negative liver cells were derived from E12.5 fetus and total thymocytes were derived from 4-6 wk old mice.
Extracted molecule genomic DNA
Extraction protocol Libraries were prepared according to NEB's instructions accompanying the NEBNext ChIP-seq Library prep Kit (E6240). The purified library was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 1500
Description Pan-Cbfb ChIP-seq of total thymocytes
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: wiggle file format of mapped reads per kilobase
Submission date Dec 02, 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 (1)
GSE90794 Genome-wide maps of Cbfb variants bound regions in E12.5 lineage negative fetal liver cells and adult thymocytes.
BioSample SAMN06099208
SRA SRX2389674

Supplementary file Size Download File type/resource
GSM2412764_panCBFB_total.wig.gz 27.2 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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