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Sample GSM241142 Query DataSets for GSM241142
Status Public on Dec 01, 2007
Title LPS, 30 min, Rep_3
Sample type RNA
 
Source name IL-10 -/- bone marrow derived macrophages treated with LPS (100 ng/ml) for 30 minutes
Organism Mus musculus
Characteristics Genotype: IL-10-/-
Treatment protocol Macrophages were treated for the indicated times with LPS (100 ng/ml) or with LPS (100 ng/ml) plus IL-10 (10 ng/ml) in the presence of complete DMEM/10% FBS without CSF-1.
Growth protocol Macrophages were isolated from the bone marrow of IL-10 -/- mice and cultured in complete DMEM containing CSF-1 (source: conditioned media from L cells) and 10% fetal bovine serum for 7 days until mature macrphages constituted >95% of the viable cells. Macrophages were scraped and re-plated under identical conditions for each replicate sample. For each replicate, a complete independent experiment was performed using mice of the same age and sex. Each replicate was performed sequentially.
Extracted molecule total RNA
Extraction protocol Trizol extraction of total RNA was performed 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 Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45 °C on GeneChip Mouse Genome 430 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Scan protocol GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
Description Macrophages treated with LPS, 30 min, Replicate 3
Data processing The data were analyzed with GeneChip Operating Software version 1.4 (GCOS v1.4) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
 
Submission date Nov 02, 2007
Last update date Aug 02, 2019
Contact name Peter J Murray
Organization name St. Jude Children's Research Hospital
Department Infectious Diseases
Street address 332 Nth Lauderdale
City Memphis
State/province TN
ZIP/Postal code 38105
Country USA
 
Platform ID GPL1261
Series (1)
GSE9509 A transcriptional repressor and co-repressor induced by the STAT3-regulated anti-inflammatory signaling pathway.
Relations
Reanalyzed by GSE119085
Reanalyzed by GSE135324

Data table header descriptions
ID_REF
VALUE MAS5.0 signal intensity
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 '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 195.8 P 0.004484
AFFX-BioB-M_at 325.4 P 0.00006
AFFX-BioB-3_at 215.8 P 0.000446
AFFX-BioC-5_at 603.5 P 0.000195
AFFX-BioC-3_at 880.1 P 0.000052
AFFX-BioDn-5_at 1585 P 0.000052
AFFX-BioDn-3_at 2949.2 P 0.000127
AFFX-CreX-5_at 8364.7 P 0.000052
AFFX-CreX-3_at 11300.6 P 0.000044
AFFX-DapX-5_at 664.9 P 0.000081
AFFX-DapX-M_at 1304.3 P 0.000509
AFFX-DapX-3_at 1265.4 P 0.00006
AFFX-LysX-5_at 112.8 P 0.00007
AFFX-LysX-M_at 142.7 P 0.020022
AFFX-LysX-3_at 348.2 P 0.000195
AFFX-PheX-5_at 142.8 P 0.000446
AFFX-PheX-M_at 166 P 0.000581
AFFX-PheX-3_at 223.8 P 0.000225
AFFX-ThrX-5_at 175 P 0.000972
AFFX-ThrX-M_at 251.8 P 0.000081

Total number of rows: 45101

Table truncated, full table size 1210 Kbytes.




Supplementary file Size Download File type/resource
GSM241142.CEL.gz 3.8 Mb (ftp)(http) CEL
Processed data included within Sample table

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