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Sample GSM338335 Query DataSets for GSM338335
Status Public on Oct 01, 2009
Title Monocytes_100 nM AM580 48h_donor1
Sample type RNA
Source name Monocytes from donor1 treated for 48h with 100nM AM580
Organism Homo sapiens
Characteristics Monocytes were isolated from healthy donor1 with inform consent and treated in vitro with DMSO for 48h and 100nM AM580 during the last 24h
Biomaterial provider Etablissement Français du Sang (EFS)
Treatment protocol Human peripheral-blood monocytes were obtained from the Etablissement Français du Sang (Besançon, France). Briefly, mononuclear cells were isolated by Ficoll gradient centrifugation and monocyte negative selection was performed via magnetic activated cell sorting using the Monocyte Isolation Kit II (Miltenyi Biotec, Bergisch Gladbach, Germany) according to the manufacturer’s instructions.
Growth protocol Cells were grown in RPMI 1640 medium with glutamax-I (Invitrogen, Paisley, UK) supplemented with 10% (vol/vol) fetal bovine serum (FBS; Invitrogen) in an atmosphere of 95% air and 5% CO2 at 37°C.
Extracted molecule total RNA
Extraction protocol Human total RNA was isolated with the use of Trizol (Sigma-Aldrich). RNA quality and integrity were determined using the Agilent RNA 6000 Nano Kit on the Agilent 2100 Bioanalyzer (Agilent Technologies). RNA was quantified by measuring A260nm on the ND-1000 Spectrophotometer (NanoDrop Technologies).
Label Cy3
Label protocol Sample labeling was performed as detailed in the “One-Color Microarray-Based Gene Expression Analysis protocol (version 5.5, part number G4140-90040). Briefly, 1 µg of each total RNA samples was used for the amplification and labeling step using the Agilent Low RNA Input Linear Amp Kit (Agilent Technologies) in the presence of cyanine 3-CTP (Perkin Elmer). Yields of cRNA and the dye-incorporation rate were measured with the ND-1000 Spectrophotometer (NanoDrop Technologies).
Hybridization protocol The hybridization procedure was performed according to the the “One-Color Microarray-Based Gene Expression Analysis protocol (version 5.5, part number G4140-90040) using the Agilent Gene Expression Hybridization Kit (Agilent Technologies). Briefly, 1.65 µg Cy3-labeled fragmented cRNA in hybridization buffer was hybridized overnight (17 hours, 65 °C) to Agilent Whole Human Genome Oligo Microarrays 4x44K using Agilent’s recommended hybridization chamber and oven. Following hybridization, the microarrays were washed once with 6x SSPE buffer containing 0.005% N-lauroylsarcosine for 1 min at room temperature followed by a second wash with preheated 0.06x SSPE buffer (37 °C) containing 0.005% N-lauroylsarcosine for 1 min. The last washing step was performed with acetonitrile for 30 sec.
Scan protocol Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (Agilent Technologies). The Agilent Feature Extraction Software (FES) was used to read out and process the microarray image files.
Description All the experiments from RNA extraction to data processing were performed by Miltenyi Biotec Microarray Service (Cologne)
Data processing For determination of differential gene expression FES derived output data files were further analyzed using the Rosetta Resolver gene expression data analysis system (Rosetta Biosoftware).
Submission date Oct 29, 2008
Last update date Oct 31, 2008
Contact name Cédric REBE
Organization name IFR100
Department Hopital du Bocage
Lab batiment B2
Street address 2 av marechal de Lattre de Tassigny
ZIP/Postal code 21000
Country France
Platform ID GPL4133
Series (1)
GSE13407 Effect of T0901317, AM580 or T0901317+AM580 on monocyte gene expression

Data table header descriptions
VALUE gProcessedSignal for AM580 treated monocytes from donor1

Data table
1 1.180737e+005
2 2.300016e+000
3 2.339529e+000
4 2.374662e+000
5 2.406686e+000
6 2.435576e+000
7 2.460734e+000
8 2.483292e+000
9 2.502318e+000
10 2.518659e+000
11 2.532281e+000
12 1.577223e+003
13 2.970873e+002
14 2.361033e+003
15 2.082980e+002
16 5.044214e+004
17 5.947868e+001
18 5.519520e+002
19 8.475795e+004
20 2.141537e+001

Total number of rows: 45015

Table truncated, full table size 868 Kbytes.

Supplementary file Size Download File type/resource
GSM338335.txt.gz 6.5 Mb (ftp)(http) TXT
Processed data included within Sample table

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