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Status |
Public on Mar 23, 2012 |
Title |
WT.unstim.1 |
Sample type |
RNA |
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|
Source name |
Bone marrow-derived macrophages
|
Organism |
Mus musculus |
Characteristics |
strain: C57BL/6J cell type: BMDM genotype/variation: wild type agent: none gender: female age: 8-12 weeks
|
Treatment protocol |
On day seven, for samples intended for LPS stimulation, LPS (List Biological Labs) was introduced into the culture medium, at 10 ng/mL. Cells were then incubated for 4 hours. Stimulation of the cells was verified by the presence of TNF in the culture supernatants detected by ELISA (Duoset ELISA System, R&D Systems)
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Growth protocol |
Bone marrow cells collected from femurs were plated on non-tissue culture-treated plastic in complete RPMI medium [RPMI 1640 (Cellgro) containing L-glutamine, supplemented with 10% (v/v) FBS (Hyclone), 100 IU/mL penicillin (Cellgro) and 100 μg/mL streptomycin (Cellgro)] plus 50 ng/mL recombinant human macrophage colony-stimulating factor (rhM-CSF, Chiron) (hereafter, BMDM medium). On day four, the medium was replaced, and on day six, adherent cells were lifted in PBS + 1 mM EDTA, counted, pelleted, resuspended in BMDM medium, and plated into six-well tissue culture plates.
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was isolated using TRIzol (Invitrogen). RNA quality was analyzed with an Agilent 2100 Bioanalyzer.
|
Label |
biotin
|
Label protocol |
mRNA was labeled using the Affymetrix One-Cycle Target Labeling protocol and reagents for eukaryotic target preparation
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Hybridization protocol |
The labeled cRNA was hybridized to an Affymetrix GeneChip Mouse Genome 430 2.0 array using standard protocols and reagents from Affymetrix
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Scan protocol |
Probe intensities were measured using the Affymetrix GeneChip Scanner 3000
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Description |
WT.unstim.1.CEL
|
Data processing |
Scanned images were processed into CEL files using the Affymetrix GeneChip Operating Software Probe-level intensities were background-adjusted, quantile-normalzed, and probeset-summarized using the justRMA procedure in the affy package v1.26.1 in Bioconductor v2.6, using probeset definitions from the CustomCDF project ENSG v13, loaded through the R package mouse4302mmensgcdf).
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Submission date |
Oct 03, 2011 |
Last update date |
Mar 23, 2012 |
Contact name |
Stephen Ramsey |
Organization name |
Oregon State University
|
Department |
Biomedical Sciences
|
Street address |
Dryden Hall 208A
|
City |
Corvallis |
State/province |
OR |
ZIP/Postal code |
97331 |
Country |
USA |
|
|
Platform ID |
GPL14657 |
Series (1) |
GSE32574 |
Response of Atf3-/- and WT BMDMs to treatment with LPS for 4 h |
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