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Sample GSM2417982 Query DataSets for GSM2417982
Status Public on Jul 20, 2017
Title Bcl11b_ThPOKgfpTESPE
Sample type SRA
 
Source name total thymocyte
Organism Mus musculus
Characteristics genotype/variation: Thpok gfp:dTESPE
chip antibody: anti-Bcl11b antibody (Bethyl Laboratories, A300383A)
cell type: thymocyte
Growth protocol Thymus were derived from 4-6 wk old mice.
Extracted molecule genomic DNA
Extraction 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 anti-Bcl11b antibody (Bethyl Laboratories, A300383A) that was preconjugated with magnetic beads (Dynabeads). Immunoprecipitated DNA was then purified.
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 Illumina HiSeq 1500 following the manufacturer's protocols.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 1500
 
Description S07459
Bcl11b ChIP-seq of total thymocytes from Thpok gfp:dTESPE mouse
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.
Accumulated 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 06, 2016
Last update date May 15, 2019
Contact name Takaho A. Endo
E-mail(s) takaho.endo@riken.jp
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)
GSE90949 Genome-wide maps of Bcl11b bound regions in thymocytes
GSE90990 Bcl11b hypomorphic mutant thymocytes
Relations
BioSample SAMN06113637
SRA SRX2399085

Supplementary file Size Download File type/resource
GSM2417982_Bcl11b_ThPOKgfpTESPE.wig.gz 5.8 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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