|
| Status |
Public on Jan 04, 2016 |
| Title |
AY_rep1_basal |
| Sample type |
SRA |
| |
|
| Source name |
peritoneal macrophage
|
| Organism |
Mus musculus |
| Characteristics |
cell type: peritoneal macrophage
genotype: Nrf2(AY/AY)
treatment: basal
|
| Treatment protocol |
For analysis of Nrf2-induced state, the macrophages were treated with 100-μM diethylmaleate (DEM) for 6hours
|
| 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 |
total RNA |
| Extraction protocol |
Total RNA was prepared by using RNeasy Mini Kit (QIAGEN) and 1.5 μg of total RNA was used for further steps. Isolation of poly(A)-tailed RNA and library construction were performed using SureSelect Strand Specific RNA Sample Prep Kit (Agilent Technologies).
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
AYC_vs_AYI.genes.fpkm_tracking
|
| Data processing |
Illumina bcl2fastq v2.15.0 software used for basecalling.
Reads mapped against mouse (mm10) genome using the TopHat application on Illumina BaseSpace.
Differential gene analaysis performed using Cuffdiff v2.1.1 application on Illumina BaseSpace.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each genotype were generated using Cuffdiff.
|
| |
|
| 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 |
GPL19057 |
| Series (2) |
| GSE75176 |
Comparison of expression profiles of WT and Nrf2AY/AY mutant macrophages under electrophilic stress agent [RNA-Seq] |
| GSE75177 |
Comparison of expression profiles of WT and Nrf2AY/AY mutant macrophages under electrophilic stress agent |
|
| Relations |
| BioSample |
SAMN04278888 |
| SRA |
SRX1438305 |
