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Sample GSM257673 Query DataSets for GSM257673
Status Public on Jun 27, 2008
Title Affy_Macrophage_28
Sample type RNA
 
Source name whole blood, macrophage_28
Organism Homo sapiens
Characteristics Age: 62
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 Double stranded cDNA was amplified and labelled using a biotin-NTP mix in the second IVT reaction. The labelled cRNA was then cleaned up and fragmented.
 
Hybridization protocol 15 µg of cRNA were hybridized to Affymetrix Human U133 plus 2.0 array for 16 hours at 45°C. Following hybridization, the arrays were washed and stained with streptavidin-phycoerythrin.
Scan protocol Fluorescent images recorded on a GenChip Scanner 3000 and processed with the GeneChip Operating software (Affymetrix, 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 Background correction method: Robust Mult-array Average (RMA).
Normalization: quantile
Summarization: for each probe set Median polish method was used to summarized PM intensities into on expression value
Signal intensities were log2-transformed
Detection calls were calculated using the Bioconductor package PANP(Presence-Absence calls with Negative Probesets)
 
Submission date Jan 18, 2008
Last update date Aug 28, 2018
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 GPL570
Series (2)
GSE11430 Performance comparison of Affymetrix and Illumina microarray technologies_AffymetrixDataset
GSE11540 Performance comparison of Affymetrix and Illumina microarray technologies
Relations
Reanalyzed by GSE86362
Reanalyzed by GSE119087

Data table header descriptions
ID_REF
VALUE log2-normalized expression level

Data table
ID_REF VALUE
1007_s_at 7.991735738
1053_at 8.444975737
117_at 8.685787213
121_at 8.847748319
1255_g_at 5.130676838
1294_at 9.20700811
1316_at 7.018245776
1320_at 5.471166872
1405_i_at 6.832628235
1431_at 5.075296369
1438_at 6.215667317
1487_at 8.288026652
1494_f_at 6.773247485
1552256_a_at 9.918045176
1552257_a_at 8.095128668
1552258_at 5.587773669
1552261_at 5.66148255
1552263_at 9.001317143
1552264_a_at 8.984998527
1552266_at 5.153853761

Total number of rows: 54675

Table truncated, full table size 1212 Kbytes.




Supplementary file Size Download File type/resource
GSM257673.CEL.gz 5.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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