|
| Status |
Public on Apr 02, 2014 |
| Title |
Papillary thyroid carcinoma - biological replicate 3 |
| Sample type |
RNA |
| |
|
| Source name |
Murine Papillary Thyroid Carcinoma (PTC) tumors
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Murine Papillary Thyroid Carcinoma (PTC) tumors
tumor histology: TPOCreER; BrafV600E papillary thyroid carcinoma - biological replicate 3
strain: mixed C57BL/6;129SvJae
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using Qiazol (Qiagen).
|
| Label |
biotin
|
| Label protocol |
Affymetrix GeneChip® WT Sense Target Labeling.
|
| |
|
| Hybridization protocol |
Performed according to manufacturer's instructions (Affymetrix) for Affymetrix Mouse Gene 1.0 ST arrays.
|
| Scan protocol |
Affymetrix Gene ChIP Scanner 3000 7G; GeneChip® Command Console.
|
| Data processing |
Raw hybridization intensities from Affymetrix Mouse Gene 1.0 ST arrays were normalized and summarized using the Affymetrix Power Tools software package (Affymetrix Inc., Santa Clara, CA.) to derive gene-level expression estimates (rma-sketch, MoGene-1_0-st-v1.r4.pgf, MoGene-1_0-st-v1.r4.clf, MoGene-1_0-st-v1.r4.bgp, MoGene-1_0-st-v1.r4.mps, MoGene-1_0-st-v1.r4.qcc). Multiple probe-sets targeting the same gene were collapsed using their median value. Differential gene expression analysis was performed using the Bioconductor package limma (Smyth GK, 2005) in the R environment for statistical computing (http://www.R-project.org).
|
| |
|
| Submission date |
Mar 14, 2014 |
| Last update date |
Apr 02, 2014 |
| Contact name |
A Bhutkar |
| Organization name |
MIT
|
| Street address |
77 Massachusetts Avenue
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02139 |
| Country |
USA |
| |
|
| Platform ID |
GPL6246 |
| Series (1) |
| GSE55933 |
p53 constrains progression to anaplastic thyroid carcinoma in a Braf-mutant mouse model of papillary thyroid cancer. |
|
