NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM108495 Query DataSets for GSM108495
Status Public on May 17, 2006
Title IFN gamma Macrophage_LPSstim_2h_rep1
Sample type RNA
 
Source name Bone marrow derived macrophages, stimulated LPS, 2 hours
Organism Mus musculus
Characteristics Balb/c bone marrow derrived macrophages stimulated overnight, washed, then stimulated 2 hours with 10ng/ml LPS in complete media.
Biomaterial provider Justin Edwards
Treatment protocol Bone marrow derived macrophages with IFN-gamma primed o/n at 100U/ml. 16 hours later media was removed, cells washed with PBS, then stimulated with 10ng/ml LPS.
Growth protocol Cells were growth from bone marrow progenitors in complete media (D10) containing 20% L-cell conditioned media for 7 days. Cells were plated out overnight in LCM free prior to stimulation.
Extracted molecule total RNA
Extraction protocol Trizol extraction followed by DNase treatment and RNA cleanup using RNeasy kit.
Label Biotin/Streptavidin Phycoerythrin (SAPE)
Label protocol Followed Affymetrix published Eukaryotic Sample and Array Processing manual.
 
Hybridization protocol Followed Affymetrix published Eukaryotic Sample and Array Processing manual.
Scan protocol Followed Affymetrix published Eukaryotic Sample and Array Processing manual.
Description Protocols and data processing were done using standard methods described by Affymetrix provided litterature. This includes Eukaryotic Sample and Array Processing manual and GeneChip Expression Analysis Data Analysis Fundamentals manual.
Data processing Data processing using Affymetrix Microarray Suite Version 5.0. following GeneChip Expression Analysis Data Analysis Fundamentals manual.
 
Submission date May 11, 2006
Last update date May 24, 2006
Contact name Justin Edwards
E-mail(s) jpe@umd.edu
Organization name University of Maryland
Department CBMG
Lab Mosser
Street address Blg. 231 Room 1105
City College Park
State/province MD
ZIP/Postal code 20742
Country USA
 
Platform ID GPL1261
Series (1)
GSE4811 Comparison between classically activated and type II activated macrophages to identify novel markers

Data table header descriptions
ID_REF
VALUE MAS5.0-calculated signal intensities
ABS_CALL the call in an absolute analysis that indicates if the transcript was present (P), absent (A), marginal (M), or no call (NC)
DETECTION P-VALUE p-value that indicates the significance level of the detection call

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 422.8 P 0.00141
AFFX-BioB-M_at 687.3 P 0.00034
AFFX-BioB-3_at 416.8 P 0.00034
AFFX-BioC-5_at 1404.2 P 0.00007
AFFX-BioC-3_at 1382.4 P 0.000052
AFFX-BioDn-5_at 2631.1 P 0.00007
AFFX-BioDn-3_at 6719 P 0.00006
AFFX-CreX-5_at 13823.7 P 0.000052
AFFX-CreX-3_at 18138.6 P 0.000044
AFFX-DapX-5_at 901.2 P 0.00007
AFFX-DapX-M_at 2288.3 P 0.000225
AFFX-DapX-3_at 3775.7 P 0.000044
AFFX-LysX-5_at 183.9 P 0.00039
AFFX-LysX-M_at 395.1 P 0.001796
AFFX-LysX-3_at 677.2 P 0.00011
AFFX-PheX-5_at 157 P 0.00034
AFFX-PheX-M_at 247.1 P 0.000258
AFFX-PheX-3_at 482.3 P 0.000509
AFFX-ThrX-5_at 231 P 0.003595
AFFX-ThrX-M_at 377.7 P 0.000095

Total number of rows: 45101

Table truncated, full table size 1213 Kbytes.




Supplementary data files not provided

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap