|
| Status |
Public on Apr 06, 2018 |
| Title |
Guo_099_m306, replacement |
| Sample type |
RNA |
| |
|
| Source name |
DM 6 month
|
| Organism |
Mus musculus |
| Characteristics |
treatment dose and postexposure time: DM 6 mo
animal: Male C57BL/J6
tissue: lung tissue
|
| Treatment protocol |
A stock suspension of MWCNT (1.6 mg/mL) was prepared in DM (Ca2+ and Mg2+-free phosphate-buffered saline, pH 7.4, supplemented with 5.5 mM d-glucose, 0.6 mg/mL mouse serum albumin, and 0.01 mg/mL 1,2-dipalmitoyl-sn-glycero-3-phosphocholine) with sonication as previously described by Porter et al. (2008; 2010). Serial dilutions of MWCNT suspension were made using DM as the diluent. Crocidolite asbestos (2.4 mg/mL) was suspended in DM by brief vortexing. Mice were anesthetized with isoflurane (Abbott Laboratories, North Chicago, IL). When fully anesthetized, the mouse was positioned with its back against a slant board and suspended by the incisor teeth using a rubber band. The mouth was opened, and the tongue gently pulled aside from the oral cavity. A 50 μL aliquot of sample was pipetted at the base of the tongue, and the tongue was restrained until at least 2 deep breaths were completed (but for not longer than 15 sec). Following release of the tongue, the mouse was gently lifted off the board, placed on its left side, and monitored for recovery from anesthesia. Mice received either DM; 1, 10, 40 or 80 μg MWCNT; or 120 μg asbestos.
|
| Growth protocol |
Male C57BL/J6 mice (7 weeks old, average weight 21.19 g ± 0.06 g) were obtained from Jackson Laboratories (Bar Harbor, ME). Individual mice were housed 1 per cage in polycarbonate isolator ventilated cages and provided HEPA-filtered air with fluorescent lighting from 0700 to 1900 hr. Autoclaved Alpha-Dri virgin cellulose chips and hardwood Beta-chips were used as bedding. Mice were monitored to be free of adventitous viral pathogens, parasites, mycoplasms, Helicobacter, and CAR Bacillus. Mice were maintained on Harlan Teklad Rodent Diet 7913 (Indianapolis, IN), and tap water was provided ad libitum. Animals were allowed to acclimate for at least 5 days before use.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from mouse lung tissue using a mirVana miRNA Isolation Kit from Ambion per the manufacturer's protocol. Mouse lungs were initially disrupted by transferring them to a 2 mL microcentrifuge tube containing 400 μL silica beads and 600 μL Lysis/Binding Solution.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cDNA were prepared according to the Affymetrix Plus WT kit protocol (GeneChip® WT Plus Reagent Kit Manual P/N 703174 Rev. 2) from 400 ng total RNA
|
| |
|
| Hybridization protocol |
Following labeling procedure, 2.53 ug of cDNA were hybridized at 48C on Mouse Gene ST 2.1 arrays, and were washed and stained using the Affymetrix GeneTitan system (software version 3.2.4.1515)
|
| Scan protocol |
Arrays were scanned using the Affymetrix GeneTitan system (software version 3.2.4.1515
|
| Description |
Gene expression from mouse lung tissue
|
| Data processing |
Data was analyzed using the limma and oligo Bioconductor packages implemented in the R-statistical language version 3.0.0. RMA was used to fit log2 transformed expression values
|
| |
|
| Submission date |
Apr 05, 2018 |
| Last update date |
Apr 06, 2018 |
| Contact name |
Nancy Lan Guo |
| E-mail(s) |
lguo@hsc.wvu.edu
|
| Phone |
3042936455
|
| Organization name |
West Virginia University
|
| Department |
Occupational and Environmental Health Sciences
|
| Lab |
Mary Babb Randolph Cancer Center/Guo Laboratory
|
| Street address |
2816 Health Sciences Center
|
| City |
Morgatown |
| State/province |
WV |
| ZIP/Postal code |
26506-9300 |
| Country |
USA |
| |
|
| Platform ID |
GPL17400 |
| Series (1) |
| GSE112780 |
Multiwalled carbon nanotube-induced pulmonary inflammatory and fibrotic responses and genomic changes following aspiration exposure in mice: A 1-year postexposure study. |
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