|
| Status |
Public on Dec 07, 2016 |
| Title |
Sample 35_Time Point 28d Dose 0 [set 3] |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Time Point 28d Dose 0 [set 3]
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
gender: female
age: 5-7 weeks
exposed to: rutile hydrophobic TiO2NPs of 20 nm diameter
dosage: 0ug
time point: 28d post-exposure
tissue: lung
|
| Treatment protocol |
Mice were dosed via single intratracheal instillation of 18 µg (very low), 54 µg (low dose), 162 µg (medium dose), or 486 µg (high dose) of TiO2NPs in a 40 µl suspension Tissues were collected 24h and 28 days after instillation.
|
| Growth protocol |
Five-to-seven week old female C57BL/6 mice (Jackson Laboratory, Bar Harbor, Maine) were housed in autoclaved cages, provided with water and food (2012 Teklad Global standard rodent diet) ad libitum, and were subjected to a 12 hour light/dark cycle. All animal procedures were in accordance with the guidelines of the Canadian Council for Animal Care and approved by the Health Canada Animal Care Committee.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Mice were anaesthetized under isofluorane followed by exsanguination. Murine lung, liver, and heart were removed, placed in cryovials and immediately snap frozen in liquid nitrogen. Tissues were stored at -80oC until RNA extraction was performed. Total RNA was extracted from random sections (n=5 per group) using Trizol reagent (Invitrogen) and further purified using the RNeasy Mini Kit (Qiagen) with an on-column DNase I digestion according to the manufacturer's instructions. Total RNA concentration and quality was determined using a Nanodrop 1000 Spectrophotometer and an Agilent 2100 Bioanalyzer, respectively. RNA samples used for gene expression microarray had A260/280 ratios > 2.0 and RINs > 7.0.
|
| Label |
Cy5
|
| Label protocol |
Total RNA (200ng per array) was labeled using the Agilent Quick Amp Labeling Kit, Two-Color (Agilent Cat #: 5190-0444), according to the manufacturer's instructions. Control and experimental samples were labeled with Cyanine 5-CTP; whereas universal mouse reference RNA was labeled with Cyanine 3-CTP.
|
| |
|
| Channel 2 |
| Source name |
Universal Mouse Reference RNA
|
| Organism |
Mus musculus |
| Characteristics |
sample type: 11 mouse cell lines
|
| Treatment protocol |
Mice were dosed via single intratracheal instillation of 18 µg (very low), 54 µg (low dose), 162 µg (medium dose), or 486 µg (high dose) of TiO2NPs in a 40 µl suspension Tissues were collected 24h and 28 days after instillation.
|
| Growth protocol |
Five-to-seven week old female C57BL/6 mice (Jackson Laboratory, Bar Harbor, Maine) were housed in autoclaved cages, provided with water and food (2012 Teklad Global standard rodent diet) ad libitum, and were subjected to a 12 hour light/dark cycle. All animal procedures were in accordance with the guidelines of the Canadian Council for Animal Care and approved by the Health Canada Animal Care Committee.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Mice were anaesthetized under isofluorane followed by exsanguination. Murine lung, liver, and heart were removed, placed in cryovials and immediately snap frozen in liquid nitrogen. Tissues were stored at -80oC until RNA extraction was performed. Total RNA was extracted from random sections (n=5 per group) using Trizol reagent (Invitrogen) and further purified using the RNeasy Mini Kit (Qiagen) with an on-column DNase I digestion according to the manufacturer's instructions. Total RNA concentration and quality was determined using a Nanodrop 1000 Spectrophotometer and an Agilent 2100 Bioanalyzer, respectively. RNA samples used for gene expression microarray had A260/280 ratios > 2.0 and RINs > 7.0.
|
| Label |
Cy3
|
| Label protocol |
Total RNA (200ng per array) was labeled using the Agilent Quick Amp Labeling Kit, Two-Color (Agilent Cat #: 5190-0444), according to the manufacturer's instructions. Control and experimental samples were labeled with Cyanine 5-CTP; whereas universal mouse reference RNA was labeled with Cyanine 3-CTP.
|
| |
|
| |
| Hybridization protocol |
Equal amounts of Cy5-labeled experimental cRNA and Cy3-labeled reference RNA (200ng) were co-hybridized to Agilent Sureprint Whole Mouse GE 4x44K microarray slides, according to the instructions outlined in the Agilent Two-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) Protocol. Samples were hybridized for 17 hours at 65oC and 10 rpm.
|
| Scan protocol |
Scanned on an Agilent G2565AA scanner.
|
| Data processing |
Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1). Non background subtracted median signal intensities were LOWESS normalized using the maanova library in R. Probes with technical replicates were averaged using the median.
|
| |
|
| Submission date |
May 18, 2016 |
| Last update date |
Dec 07, 2016 |
| Contact name |
Sabina Halappanavar |
| Organization name |
Health Canada
|
| Street address |
251 Sir Frederick Banting Driveway, Building 22
|
| City |
Ottawa |
| State/province |
Ontario |
| ZIP/Postal code |
K1A 0K9 |
| Country |
Canada |
| |
|
| Platform ID |
GPL7202 |
| Series (2) |
| GSE81566 |
Surface modified titanium dioxide nanoparticles induce fibrosis-like changes in lungs at high doses [set 3] |
| GSE81570 |
Surface modified titanium dioxide nanoparticles induce fibrosis-like changes in lungs at high doses |
|
