|
| Status |
Public on Mar 03, 2020 |
| Title |
1 Control mouse |
| Sample type |
RNA |
| |
|
| Source name |
control_Left Lung
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
Sex: female
treatment: vehicle control
time point: 56 days post exposure
tissue: left lung
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from whole lung tissues of control and MWCNT exposed mice 56 days post exposure (n=5 for MWCNT group, n=4 for controls). The RNA was isolated using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) and purified using RNeasy MiniKits (Qiagen, Mississauga, ON, Canada) as described by the manufacturer.
|
| Label |
Cy3
|
| Label protocol |
Total RNA of each sample was used for labeling and array hybridization as the following steps: 1) Reverse transcription with Invitrogen Superscript ds-cDNA synthesis kit; 2) ds-cDNA labeling with NimbleGen one-color DNA labeling kit;
|
| |
|
| Hybridization protocol |
Array hybridization was done using the NimbleGen 12x135K microarray followed by washing with the NimbleGen wash buffer kit
|
| Scan protocol |
Array scanning was done using the Axon GenePix 4000B microarray scanner (Molecular Devices Corporation).
|
| Description |
Control_1
|
| Data processing |
Scanned images (TIFF format) were imported into NimbleScan software (version 2.5) for grid alignment and expression data analysis. Expression data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software.
The Gene level (*_RMA.calls) files generated after normalization were imported into Agilent GeneSpring GX software (version 12.1) for further analysis.
All Targets Value (Entities where at least 5 out of 10 samples having values greater than or equal to Lower cut-off: 50.0) were only considered from the whole array. Differentially expressed genes with statistical significance between two groups were identified through Volcano Plot filtering
|
| |
|
| Submission date |
Nov 19, 2019 |
| Last update date |
Mar 03, 2020 |
| Contact name |
Anna A Shvedova |
| E-mail(s) |
[email protected]
|
| Organization name |
CDC/NIOSH
|
| Department |
HELD
|
| Lab |
EAB
|
| Street address |
1095 willowdale Rd
|
| City |
morgantown |
| State/province |
WV |
| ZIP/Postal code |
26508 |
| Country |
USA |
| |
|
| Platform ID |
GPL25968 |
| Series (2) |
| GSE140674 |
Lung Tissue Gene Expression Profiles in Mice Exposed to Multi-walled Carbon Nanotubes. |
| GSE140676 |
Lung and Whole Blood Gene Expression Profiles in Mice Exposed to Multi-walled Carbon Nanotubes |
|
