|
| Status |
Public on Nov 06, 2014 |
| Title |
Non-metastatic_rep3 |
| Sample type |
RNA |
| |
|
| Source name |
Lung, Non-metastatic_rep3
|
| Organism |
Mus musculus |
| Characteristics |
strain: BALB/c
treatment: 67NR mouse breast carcinoma cell line injected into fourth mammary fat pad of BALB/c mouse
tissue: Lung, Non-metastatic
|
| Treatment protocol |
Six days after tumor cell inoculation (or when tumors reached about 50 mm3), mice were euthanized, and lungs were perfused with PBS to completely remove blood from the lung vasculature. Cleaned lung lobes were immersed in RNAlater (Qiagen) to stabilize RNA.
|
| Growth protocol |
BALB/c mice were injected with nonmetastatic 67NR or metastatic 4T1 cells. Control (naïve) mice received PBS only.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total DNA-free RNA was prepared from PBS-perfused lungs with the RNeasy kit (Qiagen) according to the manufacturer’s protocol
|
| Label |
biotin
|
| Label protocol |
The method for prepartation of cRNA was provided by Affymetrix. Briefly, 3 ug of total RNA was converted into double-stranded cDNA using a cDNA synthesis kit SuperScript Choice (Invitrogen) and a T7-(dT) primer (Biosearch Technologies, Inc.). cDNA was purified using Sample Cleanup Module Kit (Affymetrix) and used to generate biotin labeled cRNA using an in vitro transcription kit (Enzo Diagnostics, Inc.,). The labeled cRNA was purified using Sample Cleanup Module Kit (Affymterix).
|
| |
|
| Hybridization protocol |
The method for hybridization of the arrays was provided by Affymetrix. Fifteen micrograms of cRNA was fragmented and hybridized to Mouse430v2 arrays at 45°C for 19 hours in a rotisserie oven set at 60 rpm.
|
| Scan protocol |
Arrays were washed and stained in the Affymetrix Fluidics station and scanned on GeneChip scanner 3000.
|
| Description |
Sample name: BIO116258
Gene expression of lung, Non-metastatic_rep3
|
| Data processing |
Data analysis was performed using the Affymetrix GeneChip operating system and analysis software.
|
| |
|
| Submission date |
Oct 29, 2014 |
| Last update date |
Nov 07, 2014 |
| Contact name |
Josh Kaminker |
| Organization name |
Genentech
|
| Department |
Bioinformatics and Computational Biology
|
| Street address |
1 DNA Way
|
| City |
South San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94080 |
| Country |
USA |
| |
|
| Platform ID |
GPL1261 |
| Series (1) |
|
