|
| Status |
Public on Aug 01, 2008 |
| Title |
T4E-LU |
| Sample type |
RNA |
| |
|
| Source name |
Sodium arsenite added to food: 10 ppb, 5wk; Injection: None; Diet: LRD-5001; Sodium arsenite added to drinking water: None
|
| Organism |
Mus musculus |
| Characteristics |
sodium arsenite added to food: 10 ppb, 5wk
diet: LRD-5001
|
| Treatment protocol |
Sodium arsenite at prescribed concentrations was added to food, which was repelleted, or sodium arsenite was added to water. Injections were intraperitoneal in a normal saline solution.
|
| Growth protocol |
6wk male C57BL/6 male mice were acclimated to their respective diets for 2 wk prior to treatments.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from frozen lung samples and homogenized using QiashredderTM and RNeasy® Mini Kits (Qiagen, Valencia, CA) per manufacturer's protocol. Contaminating genomic DNA was removed using DNA-free kits
(Ambion, Austin, TX) and total RNA was quantified with a NanoDrop®ND-1000 Spectrophotometer (NanoDrop Technologies, Rockland, DE). RNA quality was determined with the RNA 6000 LabChip kit Nano Assay (Agilent Technologies, Inc., Santa Clara, CA).
|
| Label |
biotin
|
| Label protocol |
Total RNA was first reverse-transcribed using T7-oligo(dT) promoter primer in the first-strand cDNA synthesis reaction. Following RNase H-mediated second-strand cDNA synthesis, the double stranded cDNA was purified and served as a template in the subsequent in vitro transcription (IVT) reaction.
|
| |
|
| Hybridization protocol |
The IVT reaction was carried out in the presence of T7 RNA Polymerase and a biotinylated nucleotide analog/ribonucleotide mix for complementary RNA (cRNA) amplification and biotin labeling. Biotinylated cRNA (15 ug) targets were then cleaned up, fragmented, and hybridized to GeneChip® array during the overnight incubation at 45oC in rotating hybridization oven.
|
| Scan protocol |
After hybridization, the arrays were stained with streptavidin-phycoerythrin in the GeneChip Fluidics station and then scanned using Affymetrix GeneChip Scanner (laser filter set at 570 nm; pixel size 2.5 um). The array image data were acquired, and the fluorescent signal intensities were quantified using Affymetrix® GCOS v. 1.2 software with following settings of quantitation parameters: Alpha1=0.05, Alpha2=0.065, Tau=0.015, Gamma1H=0.0045, Gamma1L=0.0045, Gamma2H=0.006, Gamma2L=0.006, Perturbation=1.1, Target Intensity=150.
|
| Description |
Mouse Lung LRD Diet 5wk 10ppb As Food Exposure, biological replicate E
AN080406_Sample 4.CEL
|
| Data processing |
CEL file data were normalized using RMA as implented in Bioconductor simpleaffy. Genes were selected by Rank Product (Breitling, R., 2004, FEBS Letter, 57383-92) implemented in Bioconductor RankProd at p < .05 and by ANOVA.
|
| |
|
| Submission date |
Apr 04, 2008 |
| Last update date |
Aug 28, 2018 |
| Contact name |
Thomas H Hampton |
| E-mail(s) |
Thomas.H.Hampton@Dartmouth.edu
|
| Organization name |
Geisel School of Medicine at Dartmouth
|
| Department |
Microbiology Immunology
|
| Lab |
Stanton
|
| Street address |
North College Street
|
| City |
Hanover |
| State/province |
NH |
| ZIP/Postal code |
03755 |
| Country |
USA |
| |
|
| Platform ID |
GPL1261 |
| Series (1) |
| GSE11056 |
Expression data from mouse lung |
|
| Relations |
| Reanalyzed by |
GSE119085 |
