|
| Status |
Public on Jul 18, 2017 |
| Title |
16_id_Graphite |
| Sample type |
RNA |
| |
|
| Source name |
Graphite
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: lung
gender: female
exposure: 10 ug of CNM in 50 ul of PBS
exposure method: oropharyngeal aspiration
time: 4d + 24h
|
| Treatment protocol |
mice lung tissue samples collected 24h after final exposure. Tissue samples stored in RNAlater in -80ºC
|
| Growth protocol |
Female C57BL/6 mice (7-8 weeks old) were housed in groups of four in stainless steel cages, bedded with aspen chip and were provided with standard mouse chow diet and tab water ad lib. 12 h dark/light cycle was used in the animal room temperature being 20-21 degree celcius and humidity of 40-45 %.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA isolation from the lung samples was done with TRIsure (phenol-chloroform extraction) and the quantity and purity was determined by NanoDrop spectrophotometer. Further quality check of the total RNA was performed with the Agilent BioAnalyzer, according to the manufacturer's recommendations.
|
| Label |
cy3
|
| Label protocol |
Samples were amplified using T7 RNA polymerase method and the cRNAs were further labeled with Cy3 and Cy5 dye, according to the manufacturer's recommendations.
|
| |
|
| Hybridization protocol |
Labeled cRNAs were hybridized to Agilent 2-color 60-mer oligo arrays, , according to the manufacturer's recommendations.
|
| Scan protocol |
Slides were washed and scanned with Agilent Microarray scanner G2505C, according to the manufacturer's recommendations.
|
| Description |
raw data file: US11263921_252800520993_S01_GE2_1105_Oct12_1_2.txt
|
| Data processing |
These are dual-channel arrays that have been analyzed as single-channel arrays. All raw data files are available in a tar archive on the series record.
Raw intensity values were obtained from Agilent Feature Extraction software and quality checked according to Agilent standard procedures. The median foreground intensities were imported into R software and analyzed with BioConductor package Limma.
|
| |
|
| Submission date |
Dec 23, 2016 |
| Last update date |
Jul 18, 2017 |
| Contact name |
Dario Greco |
| E-mail(s) |
dario.greco@tuni.fi
|
| Organization name |
Tampere University
|
| Department |
Faculty of Medicine and Health Technology
|
| Lab |
Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE)
|
| Street address |
Arvo ylpön Katu 34
|
| City |
Tampere |
| ZIP/Postal code |
33520 |
| Country |
Finland |
| |
|
| Platform ID |
GPL13912 |
| Series (2) |
| GSE92900 |
Distinct Sets Of Genes Representing Overlapping Biological Functions Are Altered By Intrinsic Properties Of Carbon Nanomaterials In Vitro And In Vivo [mouse] |
| GSE92901 |
Distinct Sets Of Genes Representing Overlapping Biological Functions Are Altered By Intrinsic Properties Of Carbon Nanomaterials In Vitro And In Vivo |
|
