|
| Status |
Public on Dec 09, 2023 |
| Title |
NM401_C3_2 |
| Sample type |
RNA |
| |
|
| Source name |
THP-1 monocytes differentiated into macrophages, NM401 0.5 ug/ml IC5 replicate 2
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: THP-1
differentiation: PMA differentiated macrophage
dose: 0.5
dose unit: µg/ml
exposure time: 24 hours
treatment: NM401
samples prepared: 2021-11-18
plate: 3
rin: 9.5
|
| Treatment protocol |
Stock solution (1 mg /ml for BAY, CHT, MIT, SIG and SES, 0.5 mg/ml for NM400 and NM401) in 1 % FBS RPMI was sonicated in a bath sonicator at RT for 2 x 15 min (BAY, CHT, SIG, SES) or 3 x 15 min (MIT, NM400, NM401) and vortexed and diluted to final concentrations in 1 % FBS RPMI. Dilutions were further vortexed and sonicated for 5 minutes prior to exposure. Cells were exposed to rCNT for 24 hours. Untreated controls had the same treatment without the rCNTs. Exposures were performed as six replicates on two parallel plates for each exposure.
|
| Growth protocol |
THP-1 cells (ATCC TIB-202) were grown in culture flasks in RPMI-1640 media ( supplemented with 10% FBS, Gibco). During culturing the cell density was kept below 1x10^6 cells/ml and they were seeded three times before culturing. Cells were PMA differentiated (25 nM) for 48 hours on 12-well plates (150 000 cells/well). After differentiation, media was replaced to RPMI supplemented with 1 % FBS and the cells rested for 24 hours before exposures.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were harvested and lysed with lysis buffer (Qiagen). Two samples of the same exposure and concentration were pooled together to increase the total amount of RNA. 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 |
raw data file:
US11263921_257236348518_S01_GE2_1200_Jun14_2_4.txt
Gene expression after 24 h exposure to 0.5 ug/ml of NM401
|
| 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 |
Dec 09, 2022 |
| Last update date |
Dec 09, 2023 |
| 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 (1) |
| GSE220646 |
Intrinsic properties of MWCNT affect immunotoxicity in THP-1 in vitro model |
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