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Sample GSM110213 Query DataSets for GSM110213
Status Public on May 25, 2006
Title IFN gamma Macrophage_LPSstim_2h_rep2
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 23, 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 552 P 0.00034
AFFX-BioB-M_at 814.4 P 0.00006
AFFX-BioB-3_at 509.7 P 0.000095
AFFX-BioC-5_at 1766.7 P 0.00007
AFFX-BioC-3_at 2268.2 P 0.000044
AFFX-BioDn-5_at 2795.6 P 0.000044
AFFX-BioDn-3_at 6606 P 0.000044
AFFX-CreX-5_at 18160.3 P 0.000044
AFFX-CreX-3_at 22127.5 P 0.000044
AFFX-DapX-5_at 448.6 P 0.000195
AFFX-DapX-M_at 1233.6 P 0.00039
AFFX-DapX-3_at 2567.5 P 0.000052
AFFX-LysX-5_at 128.3 P 0.000127
AFFX-LysX-M_at 240.3 P 0.015183
AFFX-LysX-3_at 511.1 P 0.00007
AFFX-PheX-5_at 126.9 P 0.011384
AFFX-PheX-M_at 227 P 0.002556
AFFX-PheX-3_at 332.4 P 0.000095
AFFX-ThrX-5_at 137.6 P 0.006871
AFFX-ThrX-M_at 279.9 P 0.00039

Total number of rows: 45101

Table truncated, full table size 1209 Kbytes.




Supplementary data files not provided

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