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Sample GSM896443 Query DataSets for GSM896443
Status Public on Mar 15, 2013
Title Monocyte IL4 18h 3
Sample type RNA
 
Source name Monocytes stimulated with IL-4 for 18 hours
Organism Homo sapiens
Characteristics stimulation: YES
treatment: IL4
time: 18h
cell type: Monocyte
ifng: 0
il4: 1
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 IL-4 for 18 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 6.49081910613137
A_32_P77178 7.72464919306601
A_23_P212522 10.1331980044752
A_24_P934473 6.84116220883972
A_24_P9671 13.5366483538139
A_24_P801451 8.05409549039447
A_32_P30710 15.2559918048533
A_32_P86028 13.7569253617129
A_24_P470079 5.87781985405728
A_23_P65830 10.0144605342161
A_23_P109143 12.3977118653519
A_24_P391591 6.5928870878715
A_24_P835500 13.7589968855339
A_23_P67555 8.5726428627732
A_24_P286412 8.7440118912366
A_23_P202696 8.94124677919736
A_24_P927716 6.03713224091872
A_23_P124837 11.0124582554592
A_24_P329635 11.4533973511435
A_23_P148439 7.90761405487701

Total number of rows: 28931

Table truncated, full table size 834 Kbytes.




Supplementary file Size Download File type/resource
GSM896443_Monocyte-18-IL4-3.txt.gz 9.0 Mb (ftp)(http) TXT
Processed data included within Sample table

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