|
| Status |
Public on Aug 06, 2008 |
| Title |
Prostate tumor patient 20 |
| Sample type |
RNA |
| |
|
| Source name |
Adenocarcinoma (NOS) of the prostate
|
| Organism |
Homo sapiens |
| Characteristics |
race: African American
smoking status: Current
gleason sum: 7
pt stage: 3
extraprostatic extension: Focal
perineural invasion: Yes
seminal vesicle invasion: No
are surgical margins involved: All surgical margins are free of tumor
angio lymphatic invasion: No
|
| Treatment protocol |
not applicable
|
| Growth protocol |
not applicable
|
| Extracted molecule |
total RNA |
| Extraction protocol |
TRIzol
|
| Label |
biotin
|
| Label protocol |
Refer to Liu et al (PNAS 101: 9740-9744 (2004)). 5 ug of total RNA was labeled in reverse transcription at 37C for 90 mins by using biotin-labeled rand-octomer oligo primer. The RT reaction mix was further denatured by using 0.5 N NaOH / 1 mM EDTA at 65C for 15 mins and neutralized by 1 M Tris HCl pH 7.6. Biotin signal was detected with an Alexa 647-Streptavidin conjugate.
|
| |
|
| Hybridization protocol |
The chips were hybridized on Tecan HS 4800 hybridization station. Chips were pre-hybridized at 25C for 30 min in the buffer of 6x SSPE/ 30% formamide/ 1x Denhardt's solution. The chips were further hybridized with labeled target in 6x SSPE/ 30% formamide at 25C for 18 hr. Hybridization, post-hybridization washing in 0.75x TNT (Tris, sodium, Tween 20) (see PNAS) at 37C for 40 mins. The chips were stained by streptavidin-alexa647 (1:500) dilution in TNT for 30 mins. Post-staining washing in 1x TNT FOR 40 min. Rinse with water and spin dry.
|
| Scan protocol |
Arrays were scanned on the GenePix scanner and analyzed using the GenePix Pro software package.
|
| Description |
none
|
| Data processing |
median-centralized normalized data (in log scale)
|
| |
|
| Submission date |
Jun 14, 2007 |
| Last update date |
Aug 14, 2011 |
| Contact name |
Robert Scott Hudson |
| Organization name |
NIH
|
| Department |
NCI
|
| Lab |
The Laboratory of Human Carcinogenesis
|
| Street address |
National Cancer Institute Room Blgd.37/3044
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20852 |
| Country |
USA |
| |
|
| Platform ID |
GPL5180 |
| Series (1) |
| GSE8126 |
Genomic profiling of microRNA and messenger RNA reveals deregulated microRNA expression in prostate cancer. |
|
