|
| Status |
Public on Jul 26, 2019 |
| Title |
153C_550_wb 2 |
| Sample type |
RNA |
| |
|
| Source name |
Month 12, DM
|
| Organism |
Mus musculus |
| Characteristics |
strain/background: C57BL/J6
gender: Male
tissue: Blood
treatment: DM
time: Month 12
|
| Treatment protocol |
Each component consisted of 8 mice per exposure group (dispersion media [DM, negative control]; 1, 10, 40, or 80 μg MWCNT; 120 μg crocidolite asbestos [positive control]) to be sacrificed at 1, 6 or 12 months post-exposure, for a total of 144 mice.
|
| Growth protocol |
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 adventitious viral pathogens, parasites, mycoplasms, Helicobacter, and CAR Bacillus.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from mouse blood using a mirVana miRNA Isolation Kit from Ambion per the manufacturer's protocol.
|
| Label |
Oyster-550 fluorescent dye
|
| Label protocol |
The total RNA was DNase digested and low-molecular weight (LMW) RNA was isolated by ultrafiltration through YM-100 columns (Millipore) and subsequent purification using the RNeasy MinElute Clean-Up Kit (Qiagen). The LMW RNA samples were 3’-end labeled with Oyster-550 fluorescent dye using the Flash Tag RNA labeling Kit (Genisphere).
|
| |
|
| Hybridization protocol |
Labeled LMW RNA samples were hybridized to the MicroRNA microarrays according to conditions recommended in the Flash Tag RNA labeling Kit manual.
|
| Scan protocol |
The microarrays were scanned on an Axon GenePix 4000B scanner, and data was extracted from images using GenePix V4.1 software.
|
| Description |
raw data file: 2013-09-26_19723153_550PMT_5um_0532.txt, Array C (blocks 17-24)
|
| Data processing |
Data for 4 arrays were extracted from a single microarray image into a single text file using GenePix version 4.1 software. The raw text files were split in to eighteen subfiles based on block assignment, namely blocks 1-8 contained data for array A, blocks 9-16 contained data for array B, blocks 17-24 contained data for array C, and blocks 25-32 contained data for array D. Spot intensities were obtained for the 10240 features on each microarray by subtracting the median local background from the median local foreground for each spot. Visually flagged spots were removed prior to averaging and normalizing. The 95th percentile of the negative control spots was also calculated for each array. The spot intensities and 95th percentile of negative controls (TPT95) were transformed by taking the log (base 2) of each value. The detection threshold (T) for each microarray was computed by summing five times the standard deviation of the background signal and the 10% trim mean of the negative control spots. The mean probe intensities for each of the probes on each array were then determined by averaging the triplicate spot intensities. Spots that have an average saturated signal were removed prior to normalization. The normalization factor (N) for each microarray was determined by obtaining the 20% trim mean of the non-saturated human probes above threshold in all samples. The log2-transformed spot intensities for all features were normalized, by subtracting N from each spot intensity, and scaled by adding the grand mean of N across all microarrays.
|
| |
|
| Submission date |
Apr 21, 2019 |
| Last update date |
Jul 26, 2019 |
| 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 |
GPL26525 |
| Series (2) |
| GSE130109 |
miRNA profiling of blood samples from MWCNT exposed mice |
| GSE131123 |
miRNA profiling of MWCNT exposed mice |
|
