|
| Status |
Public on Jan 26, 2016 |
| Title |
H2O2-10-3d-Replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
Bronchial epithelial cell
|
| Organism |
Homo sapiens |
| Characteristics |
experiment: 1
cell type: BEAS2B cells
treatment: 150 uM H2O2 added and then cultured at 10 % O2 tension in vitro for 3 days
|
| Treatment protocol |
The cells cultured at 10% O2 were incubated in Panasonic MCO-5M-PA O2/CO2 incubator equipped with zirconia sensor and automatic O2 cylinder switch over system for constant moitoring and maintanence of O2 levels. CO2 levels were maintained at 5% in both the conditions. The cells and the media were pre-equilibriated at 10% O2 for 24 hrs before the start of each experiment. The cells were cultured at 10% O2 and 21% O2 for 3 days (acute) and 3 weeks (chronic). For H2O2 exposure, BEAS-2B cells were treated with 150 µM H2O2 for 3 days.
|
| Growth protocol |
Immortalized human bronchial epithelial cells (BEAS-2B) were cultured as previously reported in Dulbecco’s modified Eagle’s medium (DMEM) (Cellgro), supplemented with 1% (vol/vol) penicillin–streptomycin and 10% (vol/vol) FBS (Atlanta Biologicals) at 37 °C. For 21% O2 cultures, the cells were incubated in a standard incubator (NuAire NU-8700 AutoFlow water jacketed CO2 incubator).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from cells cultured at different O2 levels using RNeasy kit (Qiagen)
RNASeq libraries were prepared using Illumina TruSeq RNA Sample Preparation Kit (RS-122-2002), according to the manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Illumina Casava1.8 software used for basecalling.
RNA-Seq data analysis was performed using Biowardrobe experimental management system. Breifly Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh37/hg19 whole genome using STAR version 2.4.oj using default parameters; multi hits removed
Gene expression levels were quantified as reads per kilobase of exon per million fragments mapped (RPKM) using Biowardrobe algorithm
Differential gene expression was calculated using DESeq2
More information on Biowardrobe suite can be found at https://www.biowardrobe.com/
Genome_build: Feb. 2009 (GRCh37/hg19)
Supplementary_files_format_and_content: csv file include RPKM values for each Sample
|
| |
|
| Submission date |
Apr 28, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Suresh Cuddapah |
| E-mail(s) |
Suresh.Cuddapah@nyumc.org
|
| Organization name |
New York University Langone Medical center
|
| Department |
Environmental Sciecne
|
| Street address |
57 Old Forge Road
|
| City |
Tuxedo |
| State/province |
New York |
| ZIP/Postal code |
10987 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE68378 |
Ambient O2 pressure induces NF-kB1/RelA related inflammatory response in human lung epithelial cells in vitro |
|
| Relations |
| BioSample |
SAMN03571246 |
| SRA |
SRX1013088 |
