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Sample GSM1958530 Query DataSets for GSM1958530
Status Public on Dec 01, 2019
Title ChIP-Seq input for H3K4me1, H3K4me3, H3K27Ac rep 2
Sample type SRA
 
Source name BMMCs_untreated_input
Organism Mus musculus
Characteristics strain: C57BL/6
cell type: Bone marrow derived mast cells (BMMCs)
passages: >95% FcER1+ CD117+
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 SAMN04302815
SRA SRX1456412

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data not provided for this record

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