|
| Status |
Public on Mar 05, 2021 |
| Title |
MQ72_5_r3 |
| Sample type |
RNA |
| |
|
| Source name |
THP-1 monocytes differentiated into macrophages, rCNT, 5 µg/ml, 72 hours, replicate 3
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: THP-1 monocytes
differentiation: PMA differentiated macrophage
dose: 5 µg/ml
exposure time: 72 hours
treatment: rCNT
|
| Treatment protocol |
Stock solution (1mg of rCNT /ml of RPMI) was vortexed and sonicated in a bath sonicator at RT for 3 x 15 min and diluted to final concentrations of 5, 10 and 20 µg/mL with complete RPMI. Dilutions were further vortexed and sonicated for 15 minutes prior to exposure. Cells were exposed to rCNT for 24, 48 or 72 hours. Untreated controls had the same treatment without the rCNTs. Exposures were performed as triplicates.
|
| Growth protocol |
THP-1 cells (DSMZ ACC 16) were grown in culture flasks in RPMI media ( supplemented with 10% FBS, 2 mM ultraglutamine and 1% penicillin-streptomycin, Gibco). Cells were PMA differentiated (50 nM) for 48 hours on six-well plates (1.0x10^6 cells/well). Media was replaced at 24 hours for fresh, complete RPMI including PMA. After 48h PMA was removed by fresh media without PMA.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were harvested and lysed with lysing buffer (Qiagen). Total RNA was extracted and purified with the Rneasy Mini Kit by Qiagen following the kits' instructions.
|
| Label |
Cy5
|
| Label protocol |
Samples were amplified using the T7 RNA polymerase method. cRNAs were labelled with Cy3 or Cy5 following the manufacturer's protocol (Agilent).
|
| |
|
| Hybridization protocol |
Labeled cRNA samples were hybridised onto the Agilent 2-colour 8x60k arrays according to the manufacturer's recommendations and hybridized for 17 hours at 65°C. After hybridization, slides were washed following the manufacturer's recommendations (Agilent).
|
| Scan protocol |
Slides were scanned with Agilent microarray scanner G2505C and data were extracted using the Agilent Feature Extraction software (V12.02.2)
|
| Description |
Gene expression after 72 hours of exposure to 5 µg/ml of rCNT
|
| Data processing |
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 data were normalized with quantile normalization. This experiment was performed as a two-colour experiment, but data were analyzed as single-channel arrays. Raw data files are available as a tar archive on the series record.
|
| |
|
| Submission date |
Mar 10, 2020 |
| Last update date |
Mar 06, 2021 |
| 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 |
GPL20844 |
| Series (2) |
| GSE146708 |
Multi-omics analysis of dynamic dose-response in macrophages recapitulates multi-walled carbon nanotube -induced lung fibrosis [expression] |
| GSE146710 |
Multi-omics analysis of dynamic dose-response in macrophages recapitulates multi-walled carbon nanotube -induced lung fibrosis |
|
