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Sample GSM1958536 Query DataSets for GSM1958536
Status Public on Dec 01, 2019
Title ChIP-Seq of H3K4M3 in BMMC with DNP-BSA (50 ng/ml) for 2h rep 2
Sample type SRA
 
Source name BMMCs_DNP-BSA
Organism Mus musculus
Characteristics strain: C57BL/6
cell type: Bone marrow derived mast cells (BMMCs)
passages: >95% FcER1+ CD117+
treatment group: treated with DNP-BSA (50 ng/ml) for 2h
chip antibody: H3K4me3
chip antibody vendor: Millipore
chip antibody cat. #: 07-473
Treatment protocol IgE (0.5 ug/ml) treatment for 18 h, Ag (50 ng/ml) treatment for 2h after IgE treatment
Growth protocol 10 ng/ml IL-3 and 10 ng/ml SCF for 4-6 weeks after bone marrow isolation
Extracted molecule genomic DNA
Extraction protocol CHIP-seq libraries were prepared with NEB NEXT Ultra kit using 10 ng starting material
Single read - Illumina
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
 
Data processing Basecalls performed using CASAVA
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie version 0.12.7 with the following configurations : -v 2 -m 1 -p 2 --best --strata --quiet –solexa1.3-quals
Peak calling was done by MACS 2.0.10 with default settings
Genome_build: mm9
Supplementary_files_format_and_content: broadpeak files were generated by MACS 2.0.10
 
Submission date Nov 30, 2015
Last update date Dec 01, 2019
Contact name Jingxian Zhang
E-mail(s) zhangjingxian.nus@gmail.com
Organization name Institute of Molecular and Cell Biology (IMCB), A-Star, Singapore
Department IMCB
Street address 61 Biopolis Drive Proteos
City Singapore
State/province Singpaore
ZIP/Postal code 138673
Country Singapore
 
Platform ID GPL19057
Series (2)
GSE75525 Epigenetic profiling of mouse bone marrow derived mast cells (BMMCs) [ChIP-seq]
GSE111547 Landscape of mouse mast cell chromatin: a rich resource for identification of novel mediators and genetic drivers of allergic and inflammatory diseases
Relations
BioSample SAMN04302821
SRA SRX1456418

Supplementary file Size Download File type/resource
GSM1958536_Ag2_H3K4M3_peaks.broadPeak_pvalue5.bed.gz 250.8 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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