|
| Status |
Public on Jul 18, 2017 |
| Title |
Baytube.24h.1 |
| Sample type |
RNA |
| |
|
| Source name |
differentiation of THP-1 monocytes into macrophages
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: THP-1
differentiation status: macrophages
exposure: 100 ug of CNM in 1ml of RPMI medium
exposure method: differentiated THP-1 cells in culture
time: 24
|
| Treatment protocol |
Cells were exposed by replacing the old media by adding 100 µg of the CNM in 1 ml of fresh complete RPMI and incubated for 6 or 24 hours
|
| Growth protocol |
THP-1 cells (ATCC TIB-202) were grown in cell culturing flasks (75 cm2) in 30 ml of RPMI 1640 media (Gibco, Thermo Fisher Scientific) supplemented with 10% fetal bovine serum (FBS), 1% penicillin-streptomycin (PEST) antibiotics and 2mM Ultraglutamine. THP-1 cells (1.5 x 106 cells/well) were differentiated with 50nm PMA (phorbol-12-myristate-13-acetate) and exposed in six-well plates
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were harvested, lysed and the total RNA was extracted and purified by Qiagen RNeasy Plus Mini Kit manual
|
| Label |
Cy5
|
| Label protocol |
T7 amplification method (Amino Allyl MessageAmp II aRNA AmplificationKit, Ambion, Carlsbad, CA, USA) was performed to synthetize antisense RNA copies (aRNA). aRNA samples were indirectly labelled either with monoreactive Cy3, Cy5 or Alexa 488.
|
| |
|
| Hybridization protocol |
labeled aRNA samples were hybridized onto Agilent Human GE 4x44K V2 microarray slides
|
| Scan protocol |
Slides were washed and scanned with GenePix 4200 AL (Molecular Devices, Sunnyvale, CA, USA).
|
| Description |
raw data file: 140117 252665222065 Area 12 Cy5 7B24h Cy3 2B6h 488 9C24h.gpr
|
| Data processing |
These arrays were triple-labeled but analyzed as single-channel arrays. All raw data files are available in a tar archive on the series record.
Image segmentation was done using GenePixPro 6.1 software (Molecular Devices). Spot intensities were calculated as the median intensity. Data were imported into R software v. 2.3, and analysed with the 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 |
GPL10332 |
| Series (2) |
| GSE92899 |
Distinct Sets Of Genes Representing Overlapping Biological Functions Are Altered By Intrinsic Properties Of Carbon Nanomaterials In Vitro And In Vivo [human] |
| GSE92901 |
Distinct Sets Of Genes Representing Overlapping Biological Functions Are Altered By Intrinsic Properties Of Carbon Nanomaterials In Vitro And In Vivo |
|
