|
| Status |
Public on May 03, 2011 |
| Title |
ACCX1 |
| Sample type |
RNA |
| |
|
| Source name |
adenoid cystic carcinoma
|
| Organism |
Homo sapiens |
| Characteristics |
specimen id: ACCX1
tissue: adenoid cystic carcinoma
tissue source: Xenograft
|
| Growth protocol |
All xenografts reported here were implanted in mice within 36 hours of tissue being removed from the human subjects. Nude mice (nu/nu) were anesthetized with intraperitoneal injection of Ketamine/Xylazine 60-80/5-10 mg/kg. Cutaneous incisions were made in the midscapular and bilateral flank regions, with a subcutaneous pocket created by blunt dissection. One to four fragments of minced tumor (1-2 mm in diameter) were placed in each pocket, with subsequent closure of the incision with surgical staples. Tumors were allowed to grow to a maximum diameter of 1 to 1.5 cm, and were then surgically harvested. Aliquots of the xenograft tumor were minced and passaged into new mice as described above.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Frozen tissue samples of ACC xenografts and corresponding human cancers were embedded in O.C.T. compound (Sakura Finetek) and subjected to cryostat sectioning. The stained frozen sections were used to direct the dissection of tumor that corresponded to > 80% tumor cellularity. These dissected subsamples were disrupted using a tissue homogenizer (Pro-200, ProScientific) in lysis buffer supplied in the RNeasy kit (Qiagen) with subsequent RNA isolation using columns and materials supplied by the manufacturer.
|
| Label |
Biotin
|
| Label protocol |
Biotinylated cRNA was generated using standard Affymetrix protocols.
|
| |
|
| Hybridization protocol |
Hybridization was performed according to standard protocols for Affymetrix HG-U133 plus 2.0 arrays.
|
| Scan protocol |
Arrays were scanned using an Affymetrix GeneChip Scanner 3000
|
| Data processing |
The data was processed through the Affymetrix Power Tools (APT) suite using quantile normalization, perfect-match vs. mismatch correction, and the PLIER algorithm.
|
| |
|
| Submission date |
Apr 30, 2011 |
| Last update date |
May 03, 2011 |
| Contact name |
Alexander Baras |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Virginia
|
| Street address |
3024 University Hospital, PO Box 800214
|
| City |
Charlottesville |
| State/province |
Virginia |
| ZIP/Postal code |
22908 |
| Country |
USA |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE28996 |
Xenograft model systems of adenoid cystic carcinoma |
|
