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Sample GSM1368208 Query DataSets for GSM1368208
Status Public on Nov 14, 2014
Title gamma8-input
Sample type SRA
 
Source name Primary gd T cells
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: thymus
age: post natal day 0-3
genotype: wild type
chip antibody: none
cell type: gamma delta T cells
Extracted molecule genomic DNA
Extraction protocol Cellular lysate was prepared by sonication in detergent-containing buffer after fixation with 0.5% formaldehyde at room temperature for 5min, and then DNA/protein complex was obtained by enzymatic digestion.
To repair ChIP-DNA and input-DNA ends, T4 DNA polymerase, Klenow enzyme and T4 polynucleotide kinase were used (New England Biolabs), and an A base was subsequently added to the 3'-end by the treatment of Klenow exo-. The adaptor ligation and the PCR amplification for 18 cycles of DNA fragments were performed with NEB Next Multiplex Oligos for Illumina (Index Primers Set1).
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 1500
 
Data processing HiSeq control software (HCS) version 2.0.10 was used for basecalling.
ChIP-seq reads were aligned with the mouse reference geneme (mm10) using the bowtie program (v1.0.0) with the following parameters: -m 1 -n 3.
Duplicate reads were removed using the samtools program (v0.1.18). 
Peaks were called using the MACS program (v1.4.2) with the following setting: -p 1e-5 --to-large.
Genome_build: mm10
Supplementary_files_format_and_content: Bed files were generated for processed data containing chromosome, regions in which peaks were located and scores calculated with MACS program.
 
Submission date Apr 11, 2014
Last update date May 15, 2019
Contact name Masataka Nakamura
E-mail(s) gdsfx460@gmail.com
Phone +81-92-642-6962
Organization name Kyushu University
Department Medical Institute of Bioregulation
Lab Division of Host Defense
Street address 3-1-1 Maidashi
City Fukuoka city
State/province Fukuoka prefecture
ZIP/Postal code 812-8582
Country Japan
 
Platform ID GPL18480
Series (1)
GSE56756 Genome-wide analysis of intracellular notch1(ICN1) targets in gamma delta T cells (gd T cells).
Relations
BioSample SAMN02726229
SRA SRX516186

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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