|
| Status |
Public on Aug 30, 2011 |
| Title |
REC5-5 |
| Sample type |
RNA |
| |
|
| Source name |
CD4+ T cells from B6.Sle1c2 mice
|
| Organism |
Mus musculus |
| Characteristics |
gender: female
age: 6 months
strain: B6.Sle1c2
cell type: CD4+ T cells
|
| Treatment protocol |
CD4+ T cells were enriched from splenocytes using magnetic bead negative selection (Miltenyi).
|
| Growth protocol |
Female mice aged 6 months under SPF conditions.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Rneasy kits (Qiagen).
|
| Label |
biotin
|
| Label protocol |
cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.).
|
| |
|
| Hybridization protocol |
Affymetrix protocol
|
| Scan protocol |
GeneChips were scanned using the Affymetrix Scanner G3000, running GeneChip Command Console Software (AGCC v1.1)
|
| Description |
Gene expression data from B6.Sle1c2 CD4+ T cells
|
| Data processing |
The microarray data analysis was based on the use of “internal standards” (generalization of the “Error Model” (Rocke and Durbin 2001) as presented elsewhere (Dozmorov and Centola 2003; Dozmorov and Lefkovits 2009); see also early variants of software packages MDAT (Knowlton, Dozmorov et al. 2004) and Bioconductor variant: http://www.bioconductor.org/packages/2.5/bioc/vignettes/diffGeneAnalysis/inst/doc/diffGeneAnalysis.pdf. Rocke, D. M. and B. Durbin (2001). A model for measurement error for gene expression arrays. J Comput Biol 8(6): 557-69. Dozmorov, I. and M. Centola (2003). An associative analysis of gene expression array data. Bioinformatics 19(2): 204-11. Dozmorov, I. and I. Lefkovits (2009). Internal standard-based analysis of microarray data. Part 1: analysis of differential gene expressions. Nucleic Acids Res 37(19): 6323-39. Knowlton, N., I. M. Dozmorov, et al. (2004). Microarray Data Analysis Toolbox (MDAT): for normalization, adjustment and analysis of gene expression data. Bioinformatics 20(18): 3687-90.
|
| |
|
| Submission date |
Aug 29, 2011 |
| Last update date |
Aug 30, 2011 |
| Contact name |
Laurence M Morel |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Florida
|
| Department |
Pathology, Immunology and Laboratory Medicine
|
| Lab |
Morel Lab
|
| Street address |
PO Box 100275
|
| City |
Gainesville |
| State/province |
FL |
| ZIP/Postal code |
32610 |
| Country |
USA |
| |
|
| Platform ID |
GPL1261 |
| Series (1) |
| GSE31702 |
CD4+ T cell gene expression in B6 vs B6.Sle1c2 mice |
|
