|
| Status |
Public on Dec 01, 2019 |
| Title |
ChIP-Seq of H3K4M3 in untreated BMMC rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
BMMCs_untreated
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cell type: Bone marrow derived mast cells (BMMCs)
passages: >95% FcER1+ CD117+
treatment group: none (untreated control)
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 |
SAMN04302830 |
| SRA |
SRX1456427 |
