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Sample GSM2439580 Query DataSets for GSM2439580
Status Public on Jul 18, 2017
Title tCNT.6h.2
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: 6
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 Cy3
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 10 Cy5 10C6h Cy3 3C6h 488 6C24h.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

Data table header descriptions
ID_REF
VALUE Log2 transformation and quantile normalization

Data table
ID_REF VALUE
1 14.31289732
2 6.733309361
3 6.678843291
4 7.157527929
5 7.109032764
6 7.868573071
7 6.979149245
8 6.721570116
9 6.444106335
10 6.498672643
11 6.665110012
12 10.32119736
13 9.109724933
14 12.87976319
15 10.39956973
16 6.706337562
17 6.533508079
18 6.774218494
19 11.79063658
20 10.32426498

Total number of rows: 45220

Table truncated, full table size 779 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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