|
| Status |
Public on Jan 31, 2011 |
| Title |
T003, human gonadotrope/null cell tumor, biological rep 3 |
| Sample type |
RNA |
| |
|
| Source name |
Human gonadotrope/null cell tumor collected at the time of transsphenoidal surgery
|
| Organism |
Homo sapiens |
| Characteristics |
tissue (group): Gonadotrope tumor
gender: M
subclass: Gonadotrope
invasive: No
recurrent: No
scan_date: 2004-07-01
|
| Treatment protocol |
With informed consent, pituitary tumor samples were obtained from patients at University of Colorado Hospital at the time of transsphenoidal surgery. Portions of the specimens not used for histology and immunohistochemistry were placed in RNAlater and stored at -80C. Gonadotrope tumors were defined as demonstrating positive immunostaining for FSH, LH, or alpha subunit in greater than 5-10% of cells. Null cell adenomas were defined by gonadotropic staining for FSH, LH, or alpha subunit in less than 5-10% of cells. Normal pituitary glands used as controls were obtained at autopsy within 2 - 18 hours of death from University of Colorado Denver Pathology Department.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Microarray targets were prepared and labeled from 300ng of total RNA using the MessageAmp Premier RNA Amplification Kit (Applied Biosystems/Ambion, Austin, TX) following the manufactures instructions.
|
| |
|
| Hybridization protocol |
standard Affymetrix procedures
|
| Scan protocol |
standard Affymetrix procedures, using the Affy GCS3000
|
| Data processing |
Hybridization intensities were quantified and normalized across all arrays using the RMA algorithm with GC adjust available as an array processing tool on Partek® Genomics Suite™ 6.5 software (St.Louis, MS). Data were filtered to remove all genes considered absent, as determined by the Affymetrix GeneChip Operating Software (GCOS), in greater than 95% of all the samples (22 out of 23 total samples). Remaining transcripts (38,932 of 54,675) were used for all subsequent statistical and visual analysis. A mixed model ANOVA was employed to estimate the batch effect and the data were adjusted using the Partek Batch Remover™ tool available on Partek Genomics Suite.
|
| |
|
| Submission date |
Jan 31, 2011 |
| Last update date |
Jan 31, 2017 |
| Contact name |
Michael Edwards |
| E-mail(s) |
michael.edwards@ucdenver.edu
|
| Phone |
303-724-6054
|
| Organization name |
UC Denver
|
| Department |
Pulmonary
|
| Street address |
12700 East 19th Avenue, Box C272
|
| City |
Aurora |
| State/province |
CO |
| ZIP/Postal code |
80045 |
| Country |
USA |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE26966 |
Identification of Growth arrest and DNA-damage-inducible gene beta (GADD45beta) as a Novel Tumor Suppressor in Pituitary Gonadotrope Tumors |
|
| Relations |
| Reanalyzed by |
GSE68015 |
| Reanalyzed by |
GSE94349 |
