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Sample GSM909349 Query DataSets for GSM909349
Status Public on Sep 19, 2012
Title Foxo3 Knock Out BMM Stimulated with Poly-IC for 2hrs 1
Sample type RNA
Source name Poly-IC-stimulated Foxo3 knock-out bone marrow macrophages
Organism Mus musculus
Characteristics background/strain: C57BL/6
genotype/variation: Foxo3 knock-out
cell type: bone marrow macrophages
treatment: poly-IC (PIC)
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 Foxo3 knock-out bone marrow macrophages stimulated with poly-IC for 2 hrs 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 4.440725352
11298 6.3258601
11302 7.341977286
11303 10.02809576
11304 5.570090597
11305 7.570069781
11307 10.32916863
11308 11.72484018
11350 8.235312707
11352 9.189090785
11354 4.156421125
11363 8.991507211
11364 10.44415324
11370 7.992625117
11409 8.598903997
11416 8.739401614
11418 5.555422515
11419 6.298491231
11421 5.035120935
11423 4.791358801

Total number of rows: 24124

Table truncated, full table size 437 Kbytes.

Supplementary file Size Download File type/resource
GSM909349_Foxo3_null_BMMs_PIC_stim_2h_1.CEL.gz 23.5 Mb (ftp)(http) CEL
Processed data included within Sample table

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