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Sample GSM108496 Query DataSets for GSM108496
Status Public on May 17, 2006
Title macrophages_stimlpsic_2hours_rep1
Sample type RNA
 
Source name macrophages, stim. LPS+immune complexes, 2 hours
Organism Mus musculus
Characteristics Balb/c bone marrow derived macrophages
Biomaterial provider Justin Edwards
Treatment protocol BMM were IFN gamma primed overnight with 100 U/ml, washed with PBS, then stimulated for 2 hours with LPS (10 ng/ml) +Immune complexes.
Growth protocol Bone marrow derived macrophages with grown from bone marrow precursers in D10 supplemented with 20% L-cell conditioned media (LCM) for 7 days. Prior to stimulation cells were plated out and grown in LCM free media overnight.
Extracted molecule total RNA
Extraction protocol Trizol extraction followed by DNase treatment and RNA cleanup using the 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 657.8 A 0.0727
AFFX-BioB-M_at 627.3 P 0.01667
AFFX-BioB-3_at 390.6 P 0.042962
AFFX-BioC-5_at 1867 P 0.000147
AFFX-BioC-3_at 1305.3 P 0.000044
AFFX-BioDn-5_at 2692.4 P 0.00006
AFFX-BioDn-3_at 6914.7 P 0.000127
AFFX-CreX-5_at 13706.5 P 0.000044
AFFX-CreX-3_at 18139.2 P 0.000044
AFFX-DapX-5_at 1043.8 P 0.00007
AFFX-DapX-M_at 3118.6 P 0.000857
AFFX-DapX-3_at 4669.1 P 0.000052
AFFX-LysX-5_at 206.2 A 0.0727
AFFX-LysX-M_at 580.9 P 0.013811
AFFX-LysX-3_at 1087.2 P 0.000225
AFFX-PheX-5_at 205.1 M 0.062929
AFFX-PheX-M_at 309.7 M 0.054213
AFFX-PheX-3_at 676.1 P 0.003595
AFFX-ThrX-5_at 106.4 A 0.559354
AFFX-ThrX-M_at 631.3 P 0.002023

Total number of rows: 45101

Table truncated, full table size 1222 Kbytes.




Supplementary data files not provided

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