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Sample GSM252481 Query DataSets for GSM252481
Status Public on Mar 20, 2008
Title Vehicle 2 hrs Donor 2
Sample type RNA
 
Source name Monocytes__Vehicle_2_hrs
Organism Homo sapiens
Characteristics Anonymous Donor
Growth protocol Human monocytes were purified from anonymous healthy donor Buffycoats obtained from Massachusetts General Hospital. Buffycoats were stored at 4°C overnight for cell isolation the following day. Monocytes were isolated by negative selection using RosetteSep (Stem Cell Technologies, 15068) according to the manufacturer’s protocol by density centrifugation over Histopaque (SIGMA, H8889). Monocytes were maintained in RPMI 1640 (Mediatech, Inc., 15-040-CV) supplemented with 10% fetal bovine serum (SIGMA, F-9423) that had been heat-inactivated. All incubations were at 37°C in a tissue culture incubator maintained at 5% CO2.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated after 2 hour treatment using QIAshredders and RNeasy miniprep kits according to the manufacturer’s protocol (QIAGEN, 79654 and 74104, respectively). Total RNA yields ranged from 1-6 mg. Residual genomic DNA was removed by DNase treatment and phenol/chloroform extraction followed by ethanol precipitation using standard techniques.
Label Biotin
Label protocol Microarray on Affymetrix Human Genome U133_plus 2.0 arrays was performed according to established protocols
 
Hybridization protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Scan protocol Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Description Sample_Treatment_[C] = Vehicle
Sample_Treatment_amount_[C] = (Not applicable)
Sample_Treatment_2_[C] = (Not applicable)
Sample_Treatment_2_amount_[C] = (Not applicable)
Sample_Treatment_Source = (Not applicable)
Sample_Treatment_2_Source = (Not applicable)
Sample_Treatment_protocol = For TREM-1 activation, tissue culture treated plates were pre-incubated with an appropriate volume of 5 mg/ml a-TREM-1 antibody (R&D Systems, MAB1278) in PBS overnight in a tissue culture incubator. Wells were washed twice with PBS immediately prior to cell addition. As a control, wells received the same treatment with an isotype-matched murine IgG1 antibody (a-E.tenella; Wyeth). For LPS treatment, gel filtration chromatography purified LPS from Salmonella enterica (SIGMA, L2262) was added to a final concentration of 1 ng/ml. In the wortmannin studies, cells in RPMI/10% FBS were pre-incubated with wortmannin (SIGMA, W1628) at a final concentration of 100 nM for 30 minutes in polypropylene tubes prior to seeding into tissue culture wells. The final DMSO concentration in control and wortmannin treated cultures was 0.1%.
Data processing GeneChips were scanned using the Affymetrix 3000 Scanner
 
Submission date Dec 20, 2007
Last update date Aug 28, 2018
Contact name Scott Jelinsky
E-mail(s) Scott.Jelinsky@pfizer.com
Phone 617-674-7272
Organization name Pfizer
Department Inflammation and Immunology
Lab Computational Precision Medicine
Street address 610 Main Street
City Cambridge
State/province MA
ZIP/Postal code 02139
Country USA
 
Platform ID GPL570
Series (1)
GSE9988 Innate immune repsonses to TREM-1 activation
Relations
Reanalyzed by GSE119087

Data table header descriptions
ID_REF
VALUE The data were analyzed with GCOS 1.0 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
ABS_CALL
DETECTION P-VALUE

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-M_at 4157.131 P 4.42873E-05
AFFX-BioDn-3_at 5377.584 P 4.42873E-05
AFFX-CreX-3_at 165.2629 P 0.00010954
AFFX-LysX-3_at 8.279149 A 0.1952664
AFFX-PheX-5_at 1.36816 A 0.7371734
AFFX-r2-Bs-dap-M_at 94.99914 P 0.000732422
AFFX-r2-Bs-thr-3_s_at 7.032168 A 0.567627
223282_at 249.7895 P 0.000244141
223289_s_at 345.4025 P 0.000244141
223314_at 390.4398 P 0.005859375
223352_s_at 28.24932 P 0.01855469
223354_x_at 133.4366 P 0.001953125
223360_at 10.28069 A 0.3037109
223363_at 102.0975 P 0.004150391
223364_s_at 4.147714 A 0.9538574
223370_at 206.9417 P 0.000244141
223376_s_at 3199.703 P 0.000244141
223389_s_at 171.4644 P 0.01074219
223393_s_at 119.4131 P 0.001220703
223411_at 150.0314 P 0.000244141

Total number of rows: 54675

Table truncated, full table size 1721 Kbytes.




Supplementary file Size Download File type/resource
GSM252481.cel.gz 7.5 Mb (ftp)(http) CEL
Processed data included within Sample table

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