|
| Status |
Public on Feb 22, 2012 |
| Title |
Dnmt3b-deficient Lymphoma, biological replicate 1 |
| Sample type |
RNA |
| |
|
| Source name |
Dnmt3b-deficient tumor cells harvested from thymic lymphoma of Dnmt3b-deficient tumor mice
|
| Organism |
Mus musculus |
| Characteristics |
strain: FVB
tissue: Thymus
cell type: lymphoma
genotype: EμSR-tTA;Teto-MYC;Teto-Cre;Rosa26LOXPEGFP;Dnmt3b-/-
tumor stage: Final Tumor
|
| Treatment protocol |
Thymi from pre-tumor mice were sorted for EGFP+ cells and placed directly into TRIzol. Final tumors were harvested and placed directly into TRIzol.
|
| Growth protocol |
Th1, Th2, Th3, 3b24-1, 3b24-2 were harvested at 24 days. All Final tumor mice were harvested when lymphoma tumor burden became apparent.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
TRIzol extraction of RNA followed by column purification by Qiagen's RNEasy kit
|
| Label |
biotin
|
| Label protocol |
Total RNA samples (300 ng) were processed using the Ambion WT Expression kit per manufacturer’s recommendations to generate sense cDNA (Ambion, Austin, TX). The cDNA was fragmented and end labeled using the GeneChip WT Terminal Labeling kit per Affymetrix instructions (Affymetrix, Santa Clara, CA).
|
| |
|
| Hybridization protocol |
Following fragmentation and end labeling, 5.0 ug of end-labeled cDNA was hybridized to Affymetrix Mouse Gene 1.0 ST Arrays at 45° for 16 hrs using an Affymetrix hybridization oven and stained using the Affmetrix 450 fluidics station per manufacturer’s recommendations.
|
| Scan protocol |
The arrays were scanned using the GeneChip Scanner 3000 7G.
|
| Description |
TEJ%F0Fy2 (3b1).CEL
gene expression data from Dnmt3b-deficient tumors
|
| Data processing |
Intensities were imported into Partek Genomics Suite software using Robust Multi-chip Averaging (RMA) background correction and quantile normalization on a linear scale. Regularized t test analysis of control versus treatment comparisons was performed using a Bayesian approach to estimate the within treatment variation among replicates using Cyber-T software
|
| |
|
| Submission date |
Jun 21, 2011 |
| Last update date |
Feb 22, 2012 |
| Contact name |
Ryan Hlady |
| E-mail(s) |
[email protected]
|
| Phone |
4025595544
|
| Organization name |
UNMC
|
| Department |
Eppley
|
| Lab |
Rene Opavsky
|
| Street address |
985950 DRC II 4020
|
| City |
Omaha |
| State/province |
Nebraska |
| ZIP/Postal code |
68198 |
| Country |
USA |
| |
|
| Platform ID |
GPL6246 |
| Series (1) |
| GSE30126 |
Expression data from normal thymocytes, 24 day pre-tumor Dnmt3b-deficient thymocytes, Wild-Type Tumors, and Dnmt3b-deficient Tumors |
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