|
| Status |
Public on Mar 23, 2012 |
| Title |
Atf3KO.unstim.1 |
| Sample type |
RNA |
| |
|
| Source name |
Bone marrow-derived macrophages
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
cell type: BMDM
genotype/variation: Atf3-/-
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)
|
| 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
|
| |
|
| Hybridization protocol |
The labeled cRNA was hybridized to an Affymetrix GeneChip Mouse Genome 430 2.0 array using standard protocols and reagents from Affymetrix
|
| Scan protocol |
Probe intensities were measured using the Affymetrix GeneChip Scanner 3000
|
| Description |
Atf3KO.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).
|
| |
|
| 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 |
|
