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Sample GSM252484 Query DataSets for GSM252484
Status Public on Mar 20, 2008
Title Vehicle 2 hrs Donor 9
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 5194.13 P 4.42873E-05
AFFX-BioDn-3_at 6772.75 P 4.42873E-05
AFFX-CreX-3_at 170.1474 P 0.000126798
AFFX-LysX-3_at 12.30973 A 0.07800179
AFFX-PheX-5_at 1.224843 A 0.7371734
AFFX-r2-Bs-dap-M_at 92.21143 P 0.000244141
AFFX-r2-Bs-thr-3_s_at 1.05722 A 0.9624023
223282_at 209.1854 P 0.000244141
223289_s_at 335.0881 P 0.000244141
223314_at 210.6055 P 0.008056641
223352_s_at 42.35756 P 0.005859375
223354_x_at 93.87303 P 0.002929688
223360_at 2.48854 A 0.7729492
223363_at 57.22596 P 0.03759766
223364_s_at 5.177703 A 0.7539062
223370_at 265.0228 P 0.000244141
223376_s_at 2652.387 P 0.000244141
223389_s_at 96.13445 P 0.008056641
223393_s_at 116.5458 P 0.01416016
223411_at 105.9675 P 0.000244141

Total number of rows: 54675

Table truncated, full table size 1722 Kbytes.




Supplementary file Size Download File type/resource
GSM252484.cel.gz 7.7 Mb (ftp)(http) CEL
Processed data included within Sample table

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