|
| Status |
Public on Jun 16, 2015 |
| Title |
T-C5x [250K_Sty] |
| Sample type |
genomic |
| |
|
| Source name |
Ovarian tumor tissue
|
| Organism |
Homo sapiens |
| Characteristics |
sample origin: Xenograft
histology: Clear cell
sample type: frozen
|
| Growth protocol |
Cells were grown in 10cm dishes and extracts were harvested at 80% confluency
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cell monolayers were lysed directly in RLT+ buffer and homogenized with Qiashredder columns (Qiagen Allprep kit). Frozen tissues were homogenized by rotor-stator directly in RLT+.
|
| Label |
biotin
|
| Label protocol |
The fragmented PCR products are labeled with a single biotin at each free 3'OH using terminal deoxynucleotidyl transferase and a dideoxy biotinylated nucleoside triphosphate.
|
| |
|
| Hybridization protocol |
The biotinylated fragments are added to a hybridization solution containing a biotinylated control oligonucletide (for quality control), and hybridized to a microarray chip overnight at 49°C.
|
| Scan protocol |
The chips are then transferred to a fluidics instrument that performs washes to remove DNA that has not hybridized to its complementary oligonucleotide probe. The bound DNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE) followed by biotinylated anti-streptavidin, followed by SAPE. Each DNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured.
|
| Description |
Ovarian tumor tissue-250KSty
|
| Data processing |
CEL files and TXT files (generated by Affymetrix GTYPE using the DM algorithm) were processed by dChip and model-based expression performed using the PM/MM model. Invariant set normalization was performed as described in Lee and Wong, Genome Biology 2001, 2(8).
|
| |
|
| Submission date |
Sep 11, 2012 |
| Last update date |
Jun 16, 2015 |
| Contact name |
Tan A Ince |
| E-mail(s) |
Tince@med.miami.edu
|
| Phone |
305-243-1782
|
| Organization name |
University of Miami - Miller School of Medicine
|
| Department |
Sylvester Cancer Center
|
| Lab |
Dr. Ince Lab - TCC
|
| Street address |
1501 NW 10th Avenue, Rm 926
|
| City |
Miami |
| State/province |
FL |
| ZIP/Postal code |
33136 |
| Country |
USA |
| |
|
| Platform ID |
GPL3720 |
| Series (2) |
| GSE40787 |
Characterization of novel ovarian tumor cell lines that retain the phenotype of primary tumors [SNP] |
| GSE40788 |
Characterization of novel ovarian tumor cell lines that retain the phenotype of primary tumors |
|
