|
| Status |
Public on Jul 12, 2012 |
| Title |
PCa_Pool_2_R3 |
| Sample type |
RNA |
| |
|
| Source name |
Prostate Cancer
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Prostate Cancer
activation agent: Tumor
sample type: Urine
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction was performed according to easymini kit manufacturer's guideline (Qiagen, Inc)
|
| Label |
FAM
|
| Label protocol |
In total, we formed 3 pools from BPH specimens and 3 from PCa, each pool containing 100 ng of RNA. RT and preamplification reactions were carried out using a GeneAmp PCR system 9700 (Applied Biosystems). For the Megaplex RT reaction, the TaqMan® MicroRNA reverse transcription kit and the Megaplex™ RT primers, human pool A v2.0 (Applied Biosystems) were used. RT product was use as imput for the preamflification reaction, performed with the Preamp Master Mix and the Megaplex 10X preamp primer mix ( Applied Biosystems). PCR was performed using the TaqMan Array Human MicroRNA set v.2.1card A and and amplification signal was detected using the 7900 FAST real time thermal cycler ( Applied Biosystems).
|
| |
|
| Hybridization protocol |
n/a
|
| Scan protocol |
n/a
|
| Description |
Tumor
PCa_2.3
microRNA profiling
|
| Data processing |
For normalization we used as the average of the the endogenous small nuclear RNAs (snRNAs): MammU6 and U48
Target microRNAs signals were normalized to endogenous snRNAs ; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_snRNAs)]
Normalized microRNAs signal was compared between Pca and BPH groups , using Mann-Whitney U test. All analisys were done using bioconductor packages (HTqPCR, gplots, ) of the R programing enviroment.
|
| |
|
| Submission date |
Jul 12, 2012 |
| Last update date |
Jul 12, 2012 |
| Contact name |
Mauricio Rodriguez-Dorantes |
| E-mail(s) |
mrodriguez@inmegen.gob.mx
|
| Phone |
525553501900
|
| URL |
http://www.inmegen.gob.mx
|
| Organization name |
National Institute Of Genomic Medicine
|
| Department |
Research
|
| Lab |
Functional Genomic Of Cancer
|
| Street address |
Periferico Sur 4124
|
| City |
Mexico City |
| State/province |
Distrito Federal |
| ZIP/Postal code |
01900 |
| Country |
Mexico |
| |
|
| Platform ID |
GPL13328 |
| Series (1) |
| GSE39314 |
Evaluation of microRNAs in urine samples as indicators of prostate cancer occurrence |
|
