|
| Status |
Public on Jun 07, 2013 |
| Title |
WT |
| Sample type |
RNA |
| |
|
| Source name |
Wild type NT2.5
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Wild type NT2.5
metastatic site preference: bone, liver, lung
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNeasy RNA purification kit (Qiagen) was used according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA.
|
| |
|
| Hybridization protocol |
Following fragmentation, cRNA were hybridized on GeneChip Mouse Genome 430 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
|
| Scan protocol |
GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
|
| Data processing |
Data in the matrix table below were analyzed with GCOS1.4 using Affymetrix default analysis settings and global scaling as normalization method. The nonparametric hypothesis-based analysis of microarrays approach of Kowalski et al., Bioinformatics, 2004 was applied, designed to address analyses of several groups based on as few as a single sample per group. This approach was applied to (quantile) normalized, within each sample type, log2 transformed expression data using the RMA approach of Irizarry et al., Biostatistics, 2003 to obtain candidate overexpressed genes. The complete set of log2 RMA normalized data were not supplied by the submitter.
|
| |
|
| Submission date |
Jun 06, 2013 |
| Last update date |
Jun 12, 2013 |
| Contact name |
Scott Kominsky |
| E-mail(s) |
kominsc@jhmi.edu
|
| Organization name |
Johns Hopkins University School of Medicine
|
| Street address |
720 Rutland Ave, Ross 209
|
| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21205 |
| Country |
USA |
| |
|
| Platform ID |
GPL1261 |
| Series (1) |
| GSE47714 |
Osteotropism in breast cancer metastasis |
|
