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Sample GSM2439589 Query DataSets for GSM2439589
Status Public on Jul 18, 2017
Title negCont.6h.4
Sample type RNA
 
Source name differentiation of THP-1 monocytes into macrophages
Organism Homo sapiens
Characteristics cell line: THP-1
differentiation status: macrophages
exposure: 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: 140122 252665222064 Area 17 Cy5 3A24h Cy3 6C6h 488 1B6h.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 14.50299753
2 6.465272156
3 6.270761088
4 6.400826902
5 6.33616531
6 6.228214753
7 6.381420647
8 6.314772914
9 6.246501501
10 6.293973064
11 6.293973064
12 10.470811
13 9.344250141
14 13.37043
15 10.80485375
16 6.696604595
17 6.529797736
18 7.969910071
19 12.26504572
20 11.29076716

Total number of rows: 45220

Table truncated, full table size 778 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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