|
| Status |
Public on Jan 13, 2020 |
| Title |
PEP_D13_rep2 [Blood miRNA] |
| Sample type |
RNA |
| |
|
| Source name |
blood, exposed, 13 days
|
| Organism |
Rattus norvegicus |
| Characteristics |
age: 9 weeks old
Sex: male
strain: Sprague-Dawley
tissue: blood
|
| Treatment protocol |
The exposed group consisted of rats housed in individual cages and exposed via full body inhalation to PEPs and gaseous pollutants emitted by laser printer B1 using the Printer Exposure Generation System (PEGS) described in detail in a previous publication (Pirela et al, 2014). (Supplementary Material, Figure S1). In summary, printer B1 was used to generate PEPs emissions by printing a 5%-page coverage monochrome document using standardized settings (Pirela et al 2014). The laser printer B1 was selected based on exposure profiles reported in our previous studies (Pirela et al., 2014). In parallel, another group of rats was exposed to HEPA filtered air. The system was configured for twelve chambers (one animal per chamber), each equipped with a port for aerosol delivery and temperature and humidity measurement, a water bottle port, and a gas sampling port. The whole exposure experiment was repeated twice, in 2016 and 2017. Animals were placed in their chambers for 1-5 hours for 5 days prior to the exposures to ensure they gradually acclimated to exposure chambers before the exposures occurred. The following week, animals were exposed to PEPs pollutants and the room HEPA-filtered air 5 hours/day for 21 consecutive days.
|
| Growth protocol |
One hundred thirty-four healthy, male, 9 weeks old Sprague-Dawley rats, weighing an average of 300 grams were purchased from Taconic Farms Inc. (Hudson, NY). The rats were allowed to acclimatize for 1 week before the studies were initiated. Baseline data was collected for 1 week before the exposures occurred. The rats were maintained on a 12-hour light/dark cycle and food and water were provided ad libitum. Upon arrival, animals were randomly assigned a unique identification number, which determines the exposure group for the animal. There were two treatment groups: a) Control group: high efficiency particulate air (HEPA) filtered air, and b) PEPs Exposure group. All the animals were treated humanely in accordance with the guiding principles on the Use of Animals in Toxicology and the Animal Care and Use Committee of Harvard University (Ethical permit No.- 04623).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from rat blood using a mirVana miRNA Isolation Kit from Ambion per the manufacturer's protocol. Rat 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 total RNA were prepared according to the Affymetrix Flashtag Biotin HSR RNA Labeling Kit protocol from 1 ug total RNA (Affymetrix Flashtag Biotin HSR RNA Labeling Kit Manual, P/N 703095 Rev. 2)
|
| |
|
| Hybridization protocol |
Following Labeling procedure, .88 ug were hybridized at 45C on miRNA-4.1 arrays, and were washed and stained using the Affymetrix GeneTitan system (software version 4.3.0.1592)
|
| Scan protocol |
Arrays were scanned using the Affymetrix GeneTitan system (software version 4.3.0.1592)
|
| Description |
Gene expression from rat blood
|
| Data processing |
TAC 4.0 was used with annotation miRNA-4_1-st-v1.annotations.20160922.csv to generate RMA expression values. Linear models were fit using the limma package of bioconductor in R version 3.4
|
| |
|
| Submission date |
Mar 06, 2019 |
| Last update date |
Jan 13, 2020 |
| Contact name |
Nancy Lan Guo |
| E-mail(s) |
[email protected]
|
| 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 |
GPL21572 |
| Series (2) |
| GSE127947 |
Printer emitted particles (PEPs) exposed rat blood miRNA expression profiling |
| GSE127951 |
Printer emitted particles (PEPs) exposed rat expression profiling |
|
