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Sample GSM343804 Query DataSets for GSM343804
Status Public on Apr 23, 2009
Title hMDM_control_24hr_1
Sample type RNA
 
Source name human monocyte-derived macrophages, control, 24hr, replicate 1
Organism Homo sapiens
Characteristics control hMDMs
Treatment protocol Human monocyte-derived macrophages (hMDMs) were separated from fractions of peripheral blood mononuclear cells (PBMCs) obtained from the blood of healthy donors using a lymphocyte separation medium density gradient. Macrophages were treated with the Newman strain of S. aureus at an MOI of 1:50 for 8, 24, and 48 hours at 37C. Untreated macrophages serve as controls.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted with the Qiagen RNeasy kit according to the manufacturer's instructions.
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).
 
Hybridization protocol cRNA were hybridized on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2004, Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Scan protocol GeneChips were scanned using an Affymetrix scanner.
Description control hMDMs
Data processing Affymetrix GeneChip Operating Software (GCOS v1.0, http://www.affymetrix.com) was used to perform the preliminary analysis of the chips. All *.cel files, representing individual replicates, were scaled to a trimmed mean of 500 to produce the *.chp files. A pivot table with all samples was created including calls, call p-value and signal intensity for each gene.
 
Submission date Nov 19, 2008
Last update date Jul 15, 2019
Contact name Addie Whitney
E-mail(s) awhitney@niaid.nih.gov
Organization name NIH/NIAID/RML
Department LHBP
Lab DeLeo
Street address 903 S 4th St
City Hamilton
State/province MT
ZIP/Postal code 59840
Country USA
 
Platform ID GPL570
Series (1)
GSE13670 Gene expression data from S. aureus-exposed macrophages
Relations
Reanalyzed by GSE49910
Reanalyzed by GSE119087
Reanalyzed by GSE134312

Data table header descriptions
ID_REF
VALUE GCOS v1 signal
ABS_CALL indicating whether the transcript was present (P), absent (A), or marginal (M)
DETECTION P-VALUE

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 292.144 P 0.00844047
AFFX-BioB-M_at 295.445 P 0.00227496
AFFX-BioB-3_at 218.334 P 0.00227496
AFFX-BioC-5_at 311.167 P 0.000753643
AFFX-BioC-3_at 250.038 P 0.000340305
AFFX-BioDn-5_at 1838.9 P 5.16732e-05
AFFX-BioDn-3_at 3894.62 P 0.000445901
AFFX-CreX-5_at 9713 P 5.16732e-05
AFFX-CreX-3_at 11943.3 P 4.42873e-05
AFFX-DapX-5_at 1132.32 P 4.42873e-05
AFFX-DapX-M_at 3222.69 P 0.000146581
AFFX-DapX-3_at 3563.15 P 4.42873e-05
AFFX-LysX-5_at 159.233 P 0.00227496
AFFX-LysX-M_at 315.299 P 0.00933744
AFFX-LysX-3_at 518.01 P 0.000195116
AFFX-PheX-5_at 222.472 P 0.000224668
AFFX-PheX-M_at 307.138 P 0.000389797
AFFX-PheX-3_at 328.76 P 0.00227496
AFFX-ThrX-5_at 318.334 P 0.000753643
AFFX-ThrX-M_at 657.738 P 0.000126798

Total number of rows: 54675

Table truncated, full table size 1624 Kbytes.




Supplementary file Size Download File type/resource
GSM343804.CEL.gz 4.9 Mb (ftp)(http) CEL
GSM343804.CHP.gz 295.5 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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