|
| Status |
Public on Mar 05, 2021 |
| Title |
MQ24_c5_2 |
| Sample type |
genomic |
| |
|
| Source name |
THP-1 monocytes differentiated into macrophages, rCNT, 5 µg/mL, 24 hours, replicate 2
|
| Organism |
Homo sapiens |
| Characteristics |
dose: 5 µg/mL
exposure time: 24 hours
cell line: THP-1
differentiation: PMA differentiated macrophage
treatment: rCNT
position: E3
matrix: 1013419220
|
| 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 |
genomic DNA |
| Extraction protocol |
DNA was extracted from the lysates using the Maxwell RSC Cultured Cell DNA Kit and Maxwell RSC instrument following the manufacturer's instructions. (Promega Corporation)
|
| Label |
Cy3, Cy5
|
| Label protocol |
Labelling was performed following standard Illumina protocol.
|
| |
|
| Hybridization protocol |
Bisulfite converted DNA was amplified, fragmented and hybridized according to manufacturer's instructions.
|
| Scan protocol |
Scanning was performed with Illumina iScan scanner.
|
| Description |
DNA methylation of PMA differentiated THP-1 macrophages after exposure to 5 µg/mL of rCNT for 24 hours
|
| Data processing |
Preprocessing was performed with the R Bioconductor package minfi. Data was normalized using the SWAN normalization method. Unmethylated and methylated signals were extracted from the normalized data.
|
| |
|
| Submission date |
Mar 06, 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 |
GPL21145 |
| Series (2) |
| GSE146551 |
Multi-omics analysis of dynamic dose-response in macrophages recapitulates multi-walled carbon nanotube -induced lung fibrosis [methylation] |
| GSE146710 |
Multi-omics analysis of dynamic dose-response in macrophages recapitulates multi-walled carbon nanotube -induced lung fibrosis |
|
