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Status |
Public on Sep 19, 2012 |
Title |
Wildtype BMM Stimulated with PIC for 2 Hrs 2 |
Sample type |
RNA |
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Source name |
Poly-IC-stimulated bone marrow macrophages
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Organism |
Mus musculus |
Characteristics |
background/strain: C57BL/6 genotype/variation: wildtype 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).
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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).
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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.
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|
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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.
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Scan protocol |
Scanning was performed using the Affymetrix GeneChip 3000 Scanner. Images were processed into CEL files with the Affymetrix GCOS software.
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Description |
Wildtype bone marrow macrophages stimulated with poly-IC for 2 hrs sample 2.
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Data processing |
Raw CEL intensity data were RMA normalized using R/Bioconductor and the MBNI custom CDF Entrez Gene version 11 package.
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Submission date |
Apr 04, 2012 |
Last update date |
Sep 19, 2012 |
Contact name |
Ayush Raman |
E-mail(s) |
ayush.raman@systemsbiology.org
|
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 |
|