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Sample GSM896448 Query DataSets for GSM896448
Status Public on Mar 15, 2013
Title Monocyte IFNG 6h 2
Sample type RNA
 
Source name Monocytes stimulated with IFN-gamma for 6 hours
Organism Homo sapiens
Characteristics stimulation: YES
treatment: IFNg
time: 6h
cell type: Monocyte
ifng: 1
il4: 0
Treatment protocol Monocytes and monocyte-derived macrophages were stimulated with 20 ng/ml recombinant human IFN-gamma (PeproTech, Neuilly-sur-Seine, France) or IL-4 (AbCys, Paris, France) for 6 or 18 hours.
Growth protocol Leukopacks from normal blood donor buffy coats were provided from the Etablissement Français du Sang (Marseille, France). Peripheral blood mononuclear cells were isolated from blood samples after deposition over a Ficoll density cushion. They were then subjected to CD14+ magnetic cell sorting using a monocyte isolation kit (Miltenyi Biotec, Paris, France). This procedure resulted in more than 95% monocyte purity, as assessed by flow cytometry. CD14+ cells (10e6 cells per assay) were differentiated into macrophages. In brief, they were incubated in RPMI 1640 containing 20 mM HEPES, 10% human serum AB+, 2 mM L-glutamine, 100 IU/ml penicillin and 100 µg/ml streptomycin (Life Technologies, Saint Aubin, France) for 3 days, and fetal calf serum was substituted by human serum for 4 supplementary days. More than 95% of the cells were macrophages, as assessed by CD68 expression and CD14 down-modulation.
Extracted molecule total RNA
Extraction protocol RNA was extracted using an RNeasy Mini kit (Qiagen, Courtaboeuf, France). The quantity and quality of total RNA were assessed using the Nanodrop (Thermo Scientific, Illkirch, France) and a 2100 Bioanalyzer (Agilent Technologies, Massy, France). The RNA was eluted in 30 µl of water and stored at -20°C.
Label Cy3
Label protocol In brief, 250 ng RNA were labeled with cyanine-3-CTP using the Low RNA Input Fluorescent Amplification Kit from Agilent Technologies.
 
Hybridization protocol RNA was analyzed using microarray chips including 45,000 probes (4x44K Whole Human Genome, Agilent Technologies) and One-color Microarray Based Gene Expression Analysis. Hybridization was performed at 65°C using the in situ Hybridization Plus kit (Agilent Technologies) for 17 hours..
Scan protocol he arrays were scanned with a pixel size of 5 µm with the DNA Microarray Scanner G2505B. Image analysis and correction of intra-array signals were performed with the Feature Extraction Software A.9.1.3 (Agilent Technologies).
Description Monocytes stimulated with IFN-gamma for 6 hours
Data processing Microarray data analysis was performed using the R and the Bioconductor software suite. Raw data were filtered for probes with signals below background and normalized using the Agi4x44PreProcess library. Unsupervised and supervised analyses were done using hierarchical clustering, principal component analysis (PCA) (made4 library) and Significance Analysis of Microarray (SAM) algorithm (siggenes library). Genes were considered to be differentially expressed when the false discovery rae [23] was below 1% and absolute fold change (FC) was above 2.0 in at least one of the 18 pair combinations.
the "processed signal" from feature extractor was used, with no further background correction
the normalization was done with the "quantile" algorithm as mentioned
the dataset was filtered to remove controls, spot below BG, spot not found (Agilent FLAG), and saturated spots (Agilent FLAG). For each probe, the probe ws removed if the FLAG was set TRUE in > 75% of the samples
the dataset was then summarized for replicated (identical) probes (to keep only one)
 
Submission date Mar 15, 2012
Last update date Mar 15, 2013
Contact name Julien Textoris
E-mail(s) julien.textoris@gmail.com
Phone +33 472 119 546
Organization name bioMérieux
Department Medical Diagnostic Discovery Department (MD3)
Lab Joint Research Unit - bioMérieux / HCL
Street address Hôpital Edouard herriot - Pavillon P; 5 place d'Arsonval
City Lyon
ZIP/Postal code 69437
Country France
 
Platform ID GPL6480
Series (1)
GSE36537 The multifaceted responses of human monocytes to IFN-gamma and IL-4 are not reducible to M1/M2 polarization of Macrophages

Data table header descriptions
ID_REF
VALUE Quantile normalized signal intensities (log2)

Data table
ID_REF VALUE
A_24_P66027 8.65204511261266
A_32_P77178 8.56720301357222
A_23_P212522 10.3680088047396
A_24_P934473 6.2568596239295
A_24_P9671 14.9902212381555
A_24_P801451 7.15509650827034
A_32_P30710 14.3430010862407
A_32_P86028 14.1762880004072
A_24_P470079 5.94623195186945
A_23_P65830 10.6509119175110
A_23_P109143 12.4729240592856
A_24_P391591 6.52092047608208
A_24_P835500 13.1276395963364
A_23_P67555 9.56746892080108
A_24_P286412 6.61490589773844
A_23_P202696 9.54087074399345
A_24_P927716 6.20787209120979
A_23_P124837 9.67588614409257
A_24_P329635 10.9295878096882
A_23_P148439 8.25342858880698

Total number of rows: 28931

Table truncated, full table size 834 Kbytes.




Supplementary file Size Download File type/resource
GSM896448_Monocyte-6-G-2.txt.gz 9.0 Mb (ftp)(http) TXT
Processed data included within Sample table

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