|
| Status |
Public on Nov 10, 2011 |
| Title |
HD3_KO_IL4_Hyb13 |
| Sample type |
RNA |
| |
|
| Source name |
Bone Marrow-Derived Macrophages, HDAC3-Null, IL4 Treatment
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Bone Marrow
cell type: Macrophage
genotype/variation: LysM Cre+, HDAC3 floxed
agent: IL4
|
| Treatment protocol |
Macrophages were treated with either control vehicle, 0.1% bovine serum albumin (BSA) or 10ng/mL of IL-4 for 24 hours.
|
| Growth protocol |
Bone marrow derived macrophages were obtained by culturing bone marrow from 12-16 week old male C57Bl/6J mice in 30% L929 conditioned medium for six days, changing the media on the fourth day of culture. Cells were replated on day 6, allowed to rest overnight and then treated accordingly. Control macrophages were from mice with exons 4-7 of HDAC3 floxed with loxP sites (HDAC3 floxed). HDAC3 KO macrophages were from mice expressing Cre recombinase under the control of the lysozyme M promoter and with floxed HDAC3.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using the Qiagen Rneasy Kit
|
| Label |
cy3
|
| Label protocol |
RNA was amplified and labeled using the Ovation V2 Amplification Kit (NuGEN).
|
| |
|
| Hybridization protocol |
Labeled samples were hybridized overnight to the Agilent 4X44 Whole Mouse Genome Array.
|
| Scan protocol |
Arrays were washed and then scanned with the model G2565B Agilent DNA microarray Scanner (Agilent Technologies).
|
| Description |
Raw data file: 251486828385_4.txt
|
| Data processing |
Median intensities of each element on the array were captured with Agilent Feature Extraction version 9.53 (Agilent Technologies). Quality control diagnostic plots were prepared for each array, and those failing to exhibit high-quality hybridizations were excluded from further analysis, resulting in the final dataset containing four biological replicates for each condition. The subsequent analysis was performed as previously (Rieck et al. 2009). Data was quantile normalized in R with the limma package's function normalizeBetweenArray. FDRs were calculated using the SAMR package.
|
| |
|
| Submission date |
Nov 10, 2011 |
| Last update date |
Nov 10, 2011 |
| Contact name |
Logan J Everett |
| Organization name |
U.S. Environmental Protection Agency
|
| Department |
Office of Research and Development
|
| Lab |
Center for Computational Toxicology and Exposure
|
| Street address |
109 T.W. Alexander Dr
|
| City |
RTP |
| State/province |
North Carolina |
| ZIP/Postal code |
27711 |
| Country |
USA |
| |
|
| Platform ID |
GPL4134 |
| Series (2) |
| GSE33608 |
Histone Deacetylase 3 is an Epigenomic Brake in Macrophage Alternative Activation (microarray) |
| GSE33609 |
Histone Deacetylase 3 is an Epigenomic Brake in Macropahge Alternative Activation |
|
