|
| Status |
Public on May 02, 2013 |
| Title |
High Dose Day 3, Sample.48 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Heart tissue, high-dose Printex 90, day 3
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
gender: female
tissue: heart
treatment: Printex 90 carbon black nanoparticles
dose: 162 ug
time point: day 3
sampleID: 194
|
| Treatment protocol |
Female C57BL/6 mice (Taconic, Denmark) were acquired at 5-6 weeks of age and given food (Altromin no 1324; Christian Petersen, Denmark) and water ad libitum. Printex 90 was suspended by sonication in 0.9% NaCl MilliQ water containing 10% v/v acellular bronchial alveolar lavage fluid from C57BL/6 mice. A 40 µl suspension was instilled followed by 150 μl air.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using the TRIzol reagent (Invitrogen Canada Inc., Burlington, ON, Canada), and further purified using RNeasy Mini Kits (Qiagen Inc., Mississauga, ON, Canada). RNA was quantified using a UV spectrophotometer, and quality was confirmed using the Agilent 2100 Bioanalyzer and RNA 6000 NanoLab Chip Kit (Agilent Technologies Canada Inc., Mississauga, ON, Canada).
|
| Label |
Cy5
|
| Label protocol |
Individual 200 ng aliquots of RNA from each sample were amplified and labelled using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent, (5184-3523)).
|
| |
|
| Channel 2 |
| Source name |
Universal Mouse Reference RNA
|
| Organism |
Mus musculus |
| Characteristics |
sample type: reference
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Material was purchased as total RNA (Universal Mouse Reference RNA) from Stratagene (CA, USA).
|
| Label |
Cy3
|
| Label protocol |
Individual 200 ng aliquots of RNA from each sample were amplified and labelled using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent, (5184-3523)).
|
| |
|
| |
| Hybridization protocol |
Agilent Mouse G4852A Microarrays (containing approximately 44,000 probes) were hybridized with 300 ng Cy5-labelled heart RNA and 300 ng Cy3-labelled Universal Mouse Reference RNA (Stratagene, CA, USA), used as a common reference on all arrays. Arrays were incubated for 17 hours at 65 ºC in Agilent hybridization solution and washed according to manufacturer’s instructions.
|
| Scan protocol |
Arrays were scanned on an Agilent G2505B scanner. Data were acquired using Agilent Feature Extraction software version 10.7.3.1.
|
| Description |
Sample.48
|
| Data processing |
The log2 of the ratio (sample(Cy5)/reference(Cy3)), using the median signal intensities, were normalized using lowess using the transform.madata function in the maanova library in R.
|
| |
|
| Submission date |
May 09, 2012 |
| Last update date |
May 02, 2013 |
| Contact name |
Andrew Williams |
| Organization name |
Health Canada
|
| Street address |
50 Columbine
|
| City |
Ottawa |
| State/province |
ON |
| ZIP/Postal code |
K1A OK9 |
| Country |
Canada |
| |
|
| Platform ID |
GPL4134 |
| Series (2) |
| GSE37885 |
Cardiac gene expression (random section containing both ventricles) in C57BL/6 mice intratracheally instilled with Printex 90 carbon black nanoparticles (set 1) |
| GSE37891 |
Cardiac gene and miRNA expression (random section containing both ventricles) in C57BL/6 mice intratracheally instilled with Printex 90 carbon black nanoparticles |
|
