|
| Status |
Public on Jan 04, 2016 |
| Title |
AY_rep2_ChIP |
| Sample type |
SRA |
| |
|
| Source name |
peritoneal macrophage
|
| Organism |
Mus musculus |
| Characteristics |
cell type: peritoneal macrophage
genotype: Nrf2(AY/AY)
chip antibody: Nrf2 (Cell Signaling Technology; D1Z9C)
|
| Treatment protocol |
For analysis of Nrf2-induced state, the macrophages were treated with 100-μM diethylmaleate (DEM) for 4 hours
|
| Growth protocol |
7-8 weeks of mice were received an intraperitoneal injection of 4% thioglycolate broth. Four days later, macrophages collected by intraperitoneal lavage were cultured in RPMI 1640 medium containing 10% fetal bovine serum and 1% penicillin-streptomycin.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
The cells were fixed with 1% formaldehyde for 10 min at room temperature and subsequently quenched with 0.125-M glycine. ChIP was performed with anti-Nrf2 antibody (Cell Signaling Technology; D1Z9C).The antibody incubation were pereformed overnight at 4℃.
The DNA libraries were prepared from 1.5 or 2 ng of ChIP and input samples quantified with Qubit Fluorometer (Life Technologies), using Mondrian SP+ and Ovation SP Ultralow DR Multiplex System (TaKaRa).braries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
3707AY
|
| Data processing |
Illumina bcl2fastq v2.15.0 software used for basecalling.
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie2 software.
Peaks were called using MACS version 1.4
Genome_build: mm9
Supplementary_files_format_and_content: bed files were generated using MACS.
|
| |
|
| Submission date |
Nov 19, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Masayuki Yamamoto |
| E-mail(s) |
masiyamamoto@med.tohoku.ac.jp
|
| Phone |
81-22-717-8084
|
| Organization name |
Tohoku University Graduate School of Medicine
|
| Department |
Medical Biochemistry
|
| Street address |
2-1 Seiryo-machi, Aoba-ku
|
| City |
Sendai |
| ZIP/Postal code |
980-8575 |
| Country |
Japan |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE75175 |
Comparison of expression profiles of WT and Nrf2AY/AY mutant macrophages under electrophilic stress agent [ChIP-Seq] |
| GSE75177 |
Comparison of expression profiles of WT and Nrf2AY/AY mutant macrophages under electrophilic stress agent |
|
| Relations |
| BioSample |
SAMN04278876 |
| SRA |
SRX1438293 |
