|
| Status |
Public on Oct 26, 2011 |
| Title |
LMP2A pretumor mouse 7323 |
| Sample type |
RNA |
| |
|
| Source name |
B cells purified from the spleen of 3 week old LMP2A mouse
|
| Organism |
Mus musculus |
| Characteristics |
genetic background: C57/BL6
genotype: LMP2A
cell type: B cells
|
| Treatment protocol |
Pretumor B cells were purified from the spleens of 3 week old transgenic mice using magnetic-activated cell sorting (MACS) with CD19 positive selection according to manufacturer protocols (Miltenyi). Purity of >90% was confirmed by analyzing B220 expression by flow cytometry. Tumors were dissociated between frosted glass slides. Red blood cells were lysed using 155 mM ammonium chloride, and filtered through nytex to remove debris.
|
| Growth protocol |
Mice were sacrificed when cervical lymph node tumors could be observed externally and the mice were moribund. Pretumor samples were collected at 3 weeks of age. All animals were maintained at Northwestern University’s Center for Comparative Medicine, in accordance with University animal welfare guidelines.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from tumor or pretumor cells using RNeasy RNA extraction kit from QIAGEN (Valenica, CA). RNA preps were evaluated for quality using a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). Only samples with an RNA integrity number (RIN) greater than 8.0 were used for microarray analysis.
|
| Label |
Cy3
|
| Label protocol |
RNA samples were amplified, labeled, and hybridized at the Genomics Core Facility at the Center for Genetic Medicine at Northwestern University according to Illumina protocols.
|
| |
|
| Hybridization protocol |
standard Illumina protocol
|
| Scan protocol |
An Illumina iScan was used to scan the arrays.
|
| Data processing |
GeneSpring analysis software, version GX (Agilent Technologies, Santa Clara, CA) was used for data analysis. The quantile normalization method was used for preprocessing, and the baseline was set to the median of all samples. The detection p-value was used to eliminate probes which were not significantly expressed in any sample. Probes were excluded from the analysis if none of the samples had a detection p-value greater than 0.95. To identify significant probes, the Benjamini-Hochberg false discovery rate (FDR) was used for the multiple testing correction p-value. Probes with p<0.05 and a fold change of >1.5 were considered significant.
|
| |
|
| Submission date |
Jan 27, 2011 |
| Last update date |
Oct 26, 2011 |
| Contact name |
Kathryn Bieging |
| Organization name |
Northwestern University
|
| Department |
Microbiology-Immunology
|
| Lab |
Longnecker
|
| Street address |
303 East Chicago Ave
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60611 |
| Country |
USA |
| |
|
| Platform ID |
GPL6885 |
| Series (1) |
| GSE26918 |
Total gene expression analysis of LMP2A/λ-MYC and λ-MYC tumors |
|
