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Sample GSM257940 Query DataSets for GSM257940
Status Public on Aug 31, 2008
Title RNG_Monocyte_Pool26
Sample type RNA
 
Channel 1
Source name Human monocyte labeled with Cy5
Organism Homo sapiens
Characteristics Age: 73
Gender: male
Tissue: Whole blood
Cell type: monocyte
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 For the isolation of PMBC from anti-coagulated blood and removal of dead cells, a density gradient centrifugation using Ficoll–Paque (GE Healthcare) gradient was used. PMBC were washed with PBS and the supernatant completely removed. The cell pellet was re-suspended in 80 µl of PBS/BSA buffer per 107 total cells and 10 µl of MACS CD14 (Miltenyi Biotec) were added carefully, mixed and incubated for 15 min at 6°-12°C. The cells were washed by adding 10-20X labelling volume of buffer, centrifuged at 300 g for 10 min. The cells were re-suspended in 500 µl of buffer before magnetic separation as described by the manufacturer.
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 was extracted from whole blood using RNeasy mini kit of Qiagen.
Label Cy5
Label protocol RNA was amplified and labeled with Cy5
 
Channel 2
Source name Pool of 50 different monocyte and macrophage samples
Organism Homo sapiens
Characteristics Patients 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 1µg total RNA from 50 different samples were mixed, then 750ng mixed total RNA was amplified and labelled with Cy3
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 was extracted from whole blood using RNeasy mini kit of Qiagen according to the manufacturer’s instructions.
Label Cy3
Label protocol RNA was amplified and labeled with Cy3
 
 
Hybridization protocol Hybridizations were performed using the Agilent in situ hybridization kit. For each sample, 750 ng of Cy5-labeled, linearly amplified cRNA was mixed with equal amounts of Cy3-labelled, linearly amplified reference cRNA. The mixture was then fragmented by incubation with the fragmentation buffer at 60°C for 30 minutes. An equal amount of 2x hybridization buffer was added to the fragmented cRNA mixture and hybridized to whole-genome oligo arrays (Human-25K, Réseau National des Génopoles, France) at 60°C for 17 hours
Scan protocol Fluorescent images of hybridized microarrays were obtained with a GenePix 4000 Axon Instruments scanner and provessed with the GenePix software (Axon Instruments).
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 The Bioconductor packages marray and Limma were used to perform quality control and preprocessing.
Background correction method: normexp
Within array print-tip loess normalization was performed for each spot followed by between array quantile normalization.
bad spots were not included in the analysis.
 
Submission date Jan 21, 2008
Last update date Jul 28, 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 GPL1946
Series (1)
GSE10220 Gene expression profiling of human monocytes and monocyte-derived-macrophages

Data table header descriptions
ID_REF
VALUE normalized log ratio of (test/reference)

Data table
ID_REF VALUE
1 -0.223758741
10 -0.641953596
100 -0.177115552
1000 0.01774302
10000 -0.021458362
10001 0.456873659
10002 -1.45358349
10003 0.139029051
10004 -0.269752301
10005 -0.018712876
10006 0.828643631
10007 0.162405242
10008 0.462339044
10009 0.565529951
1001 -0.052597547
10010 0.004865397
10011 -1.068940344
10012 1.392511851
10013 0.34400858
10014 0.059972043

Total number of rows: 26496

Table truncated, full table size 463 Kbytes.




Supplementary file Size Download File type/resource
GSM257940.gpr.gz 2.0 Mb (ftp)(http) GPR
Raw data provided as supplementary file
Processed data included within Sample table

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