|
| Status |
Public on Sep 26, 2012 |
| Title |
BEAS2B_2.5 μM arsenic trioxide_6month_rep2 |
| Sample type |
RNA |
| |
|
| Source name |
BEAS-2B human immortalized lung epithelial cell, 2.5 μM arsenic trioxide, 6 month exposed, replicate 2
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: immortalized lung epithelial cells (BEAS-2B)
stress: arsenic
|
| Treatment protocol |
As2O3 spiking solutions in sterile PBS were diluted in fresh media and added to culture plates. Unexposed BEAS-2B cells (2x105 cells/well) were seeded to 6-well plates. After 24 hours, cell cultures were either exposed 2.5 μM As2O3 or unexposed for the following 6 months. Spiked media was changed every 3 to 4 days while cells were split once every 7 days.
|
| Growth protocol |
Cells were maintained in DMEM medium with 5% fetal bovine serum, 2 mM L-glutamine and 100 U/mL penicillin and streptomycin. Cell cultures were held in a humid, 37o C and 5% CO2 cell culture incubator.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
B-As and B-Control cell RNA replicate samples were collected with TRIzol (Invitrogen) post-exposure using manufactorer's protocol. RNA quality was assessed in house using gel electrophoresis and 260/280 nm absorbance ratio. Samples stored at -80o C were shipped to ArrayStar (Rockville, MD). At ArrayStar, samples were treated with DNase digestion and analyzed for RNA quality using Nanodrop ND-100 and Bioanalyser 2100.
|
| Label |
Cy3
|
| Label protocol |
Samples were amplified, Cy3 labeled using Agilent Quick Amp Labeling Kit following manufactorer's protocol. Microarray hybridization was performed at 65°C for 17 hours in Agilent’s SureHyb Hybridization Chambers. After being washed in an ozone-free environment, the slides were scanned using the Agilent DNA microarray scanner (part number G2505B).
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| |
|
| Hybridization protocol |
Microarray hybridization was performed at 65°C for 17 hours on Agilent 4x44K Whole Human Genome Oligonucleotide Microarray (#014850) in Agilent SureHyb Hybridization Chambers.
|
| Scan protocol |
After washing processed slides were scanned with an Agilent G2505B DNA scanner.
|
| Description |
Genome expression after 6 month arsenic trioxide 2.5 μM in vitro exposure
Raw data file: B-As-2.txt
|
| Data processing |
Agilent Feature Extraction Software (ver. 10.5.1.1) gene expression text files were imported into GeneSpring GX (ver. 10.0) for normalization using Agilent FE one-color scenarios. Only genes marked marginal or present in all samples were used (n=20,232). Normalization was performed by taking the average intensity across replicate samples.
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| |
|
| Submission date |
Nov 07, 2011 |
| Last update date |
Sep 26, 2012 |
| Contact name |
Todd A Stueckle |
| E-mail(s) |
tstueckle@cdc.gov
|
| Phone |
304 285-6098
|
| Organization name |
National Institute for Occupational Safety and Health
|
| Department |
Health Effects Laboratory Division
|
| Lab |
Pathology and Physiology Research Branch
|
| Street address |
1095 Willowdale Road
|
| City |
Morgantown |
| State/province |
WV |
| ZIP/Postal code |
26505 |
| Country |
USA |
| |
|
| Platform ID |
GPL6480 |
| Series (1) |
| GSE33520 |
Whole genome expression profile of lung epithelial cells following chronic arsenic exposure |
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