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Sample GSM909340 Query DataSets for GSM909340
Status Public on Sep 19, 2012
Title Wildtype BMM Unstimulated 1
Sample type RNA
Source name Unstimulated bone marrow macrophages
Organism Mus musculus
Characteristics background/strain: C57BL/6
genotype/variation: wildtype
cell type: bone marrow macrophages
treatment: none
Treatment protocol For PIC stimulation, BMMs were treated for 2 hours with PIC (6μg/ml; Amersham).
Growth protocol C57BL/6 mice were obtained from Jackson Laboratories. Foxo3-/- mice in the FVB background were obtained from MMRRC and were backcrossed to C57BL/6 mice at least 5 times to generate congenic mice. C57BL/6 Foxo3+/- heterozygotes were intercrossed to generate Foxo3-/- mice. Bone marrow macrophages (BMMs) were isolated from femurs of WT C57BL/6 and Foxo3-null mice and were plated on non-tissue culture-treated plastic in complete RPMI medium containing 10% (vol/vol) FBS (Hyclone Laboratories), 2 mM L-glutamine, 100 IU/ml of penicillin and 100 g/ml of streptomycin (all from Cellgro, Mediatech) and supplemented with recombinant human macrophage colony-stimulating factor (50 ng/ml; Peprotech).
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using a Trizol solution (Invitrogen, and overall RNA quality was analyzed with an Agilent 2100 Bioanalyzer. Sample mRNA was amplified, labeled and hybridized to GeneChip Mouse Exon 1.0 ST arrays according to the array manufacturer’s instructions (Affymetrix).
Label Biotin
Label protocol 200ng of total RNA was labeled according to the Ambion WT Expression kit for Affymetrix GeneChip Whole Transcript Expression Arrays followed by the Affymetrix GeneChip WT Terminal Labeling Kit.
Hybridization protocol Labeled, fragmented cDNA was hybridized for 16 hours at 45 deg C and 60rpm to an Affymetrix GeneChip according to the Affymetrix Whole Transcript Sense Target Labeling protocol. The chips were washed and stained using fluidics protocol FS450_0001.
Scan protocol Scanning was performed using the Affymetrix GeneChip 3000 Scanner. Images were processed into CEL files with the Affymetrix GCOS software.
Description Wildtype bone marrow macrophages unstimulated sample 1.
Data processing Raw CEL intensity data were RMA normalized using R/Bioconductor and the MBNI custom CDF Entrez Gene version 11 package.
Submission date Apr 04, 2012
Last update date Sep 19, 2012
Contact name Ayush Raman
Phone 206-732-1473
Organization name Institute for Systems Biology
Department Computational Dept.
Lab Shmulevich Lab
Street address 401 Terry Avenue North
City Seattle
State/province WA
ZIP/Postal code 98105
Country USA
Platform ID GPL15408
Series (2)
GSE37051 Identification of a FOXO3/IRF7 circuit that limits inflammatory sequelae of antiviral responses (expression)
GSE37052 Identification of a FOXO3/IRF7 circuit that limits inflammatory sequelae of antiviral responses

Data table header descriptions
VALUE RMA signal estimate from Bioconductor

Data table
11287 4.351572558
11298 6.563060503
11302 7.800618732
11303 10.90063584
11304 5.623975994
11305 7.758119285
11307 10.25509081
11308 11.34389101
11350 8.91958904
11352 8.28821811
11354 4.193195974
11363 8.609094002
11364 10.67736455
11370 7.957290143
11409 8.962535453
11416 8.977484817
11418 5.599437436
11419 6.496326879
11421 5.162885351
11423 4.918270241

Total number of rows: 24124

Table truncated, full table size 437 Kbytes.

Supplementary file Size Download File type/resource
GSM909340_WT_BMMs_unstimulated_1.CEL.gz 23.5 Mb (ftp)(http) CEL
Processed data included within Sample table

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