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Sample GSM257797 Query DataSets for GSM257797
Status Public on Jun 27, 2008
Title Illum_Macrophage_21
Sample type RNA
 
Source name whole blood, macrophage_21
Organism Homo sapiens
Characteristics Age: 70
Gender: male
Tissue: whole blood
Cell type: macrophage
Patient with symptoms of acute coronary syndrome who had
undergone coronary angiography (who had one stenosis >50 % diagnosed in at least one major coronary artery)
Biomaterial provider The department of cardiology of the Pitié-Salpêtrière Hospital, Paris
Treatment protocol Blood was drawn under standardized conditions in EDTA tubes: 40 ml samples were collected immediately after coronary angiography and stored at 4°C. Monocytes isolation was performed within 2 hours after Blood drawing. After density gradient centrifugation and washing, PMBC were mixed with CD14 coated beads (MACS, Miltenyi Biotec). To induce phagocytic differentiation, a fraction of the monocytes was incubated for 6 days with macrophage colony stimulating factor (M-CSF, SIGMA).
Growth protocol The human monocytes CD14+ obtained after MACS separation were cultured at a concentration of 1x 106 cells/ml in pure RPMI 1640 medium in P6 Petri dishes. After 1h of incubation at 37°C, non adherent cells were removed and the medium was replaced with RPMI 1640 Glu+ medium supplemented with 100U/ml penicillin, 100 µg/ml streptomycin and 10 % FCS, together with 10 ng/ml of macrophage colony stimulating-factor (M-CSF, SIGMA). Cells were incubated for 6 days at 37°C/5% CO2 to induce the phagocytic differentiation.
Extracted molecule total RNA
Extraction protocol RNA extraction was done using RNAeasy minikit (Qiagen).
Label biotin
Label protocol Refer to the Illumina Gene Expression System Manual
 
Hybridization protocol 1.5 µg were hybridized to human 6 beadarrays (Illumina, CA, USA) for 16 hours at 55°C. Following hybridization, beadarrays were washed and stained with streptavidin-Cy3 (GE Healthcare, UK).
Scan protocol Fluorescent images were obtained with a Beadarray reader and processed with the BeadScan software (Illumina, CA, USA).
Description All RNA preparation were checked with Agilent Bioanalyser (RNA 6000 nano-kit) and only RNA with RNA integrity number (RIN) > 8 were accepted for RNA amplification.
Data processing Data were background subtracted using BeadStudio software. (Illumina).
Quality control and pre-processing were performed in the statistical environment R using the Bioconductor packages BeadArray and BeadExplorer Bead-averaged data was normalized using a quantile normalization method Detection scores were calculated in BeadStudio software.
 
Submission date Jan 18, 2008
Last update date Jun 27, 2008
Contact name Francois Cambien
E-mail(s) francois.cambien@upmc.fr
Fax (33) 140779728
URL http://genecanvas.idf.inserm.fr
Organization name INSERM
Department Cardiovascular Genomics
Lab INSERM U937
Street address 91 Bd de l'Hôpital
City Paris
State/province France
ZIP/Postal code 75634 Paris Cedex 13
Country France
 
Platform ID GPL6097
Series (2)
GSE10213 Performance comparison of Affymetrix and Illumina microarray technologies_IlluminaDataSet
GSE11540 Performance comparison of Affymetrix and Illumina microarray technologies

Data table header descriptions
ID_REF
VALUE log2-normalized expression level

Data table
ID_REF VALUE
360450 6.247737673
1690139 6.253989266
5420594 7.432583657
3060411 6.726831217
450341 9.295734502
5420324 6.245647774
730162 6.362469889
4200739 7.959016623
1090156 6.092968509
7050341 6.54225805
1500019 6.099084761
6860601 6.560562119
430184 9.019924261
3780725 8.688704905
1400671 6.399683809
2650605 6.20026108
1660441 8.291493053
5700086 6.269594252
1050280 10.09171306
4210093 6.417177412

Total number of rows: 47296

Table truncated, full table size 961 Kbytes.




Supplementary file Size Download File type/resource
GSM257797.txt.gz 582.7 Kb (ftp)(http) TXT
Processed data included within Sample table

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