|
| Status |
Public on Oct 17, 2014 |
| Title |
Pooled tumor, tech rep1 [set 2] |
| Sample type |
RNA |
| |
|
| Source name |
Pool of 10 patient's prostate Tumor tissues
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Pool of 10 patient's prostate Tumor tissues
tumore stage: 5 T3a, 1 T4, 1 T2c, and 3 unknown
|
| Treatment protocol |
After prostatectomy, the pathologist examined tumor part and adjacent normal part of prostate. Two biopsy needle amount tissues were obtained from 10 pair of samples and tissues were immersed in RNAlater (Ambion, Austin TX). After 24 hr at 4C, samples were stored at -80C.
|
| Growth protocol |
Cells were grown in RPMI1640 medium supplemented with 10% fetal bovine serum. Cells were harvested at confluency 70%.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were prepared using the RNeasy kit (QAIGEN, Valencia CA) following the manufacturer's recommendations. The prostate epithelial cell RNA was purchased from Biochain (Cat # R1234201-50, Newark CA). RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
|
| Label |
Cy3
|
| Label protocol |
The samples were labeled using One Color Quick Amp Labeling kit following Manufacturer's (Agilent Technologies) protocol. The protocol incorporates Cyanine 3-CTP to the target (aRNA) material.
|
| |
|
| Hybridization protocol |
The fragmented and labeled aRNA (600ng) were hybridized onto Agilent’s 8x60k format Human LINC RNA array using Agilent Technologies Gene Hybridization protocol.
|
| Scan protocol |
The arrays were scanned using Agilent's C Scanner following the scan protocol
|
| Description |
Tumor-1
Gene expression in human prostate tumor tissues
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 039494_D_F_20120628) to obtain mean signals which were background corrected, log transformed and normalized using using Limma package.
|
| |
|
| Submission date |
Mar 14, 2014 |
| Last update date |
Apr 23, 2018 |
| Contact name |
Jian-Liang Li |
| Organization name |
NIEHS
|
| Street address |
111 TW Alexander Dr
|
| City |
Durham |
| State/province |
NC |
| ZIP/Postal code |
27709 |
| Country |
USA |
| |
|
| Platform ID |
GPL16699 |
| Series (2) |
| GSE55909 |
Long noncoding RNA as putative biomarkers for protstate cancer detection [Set 2] |
| GSE55910 |
Long noncoding RNA as putative biomarkers for protstate cancer detection |
|
| Relations |
| Reanalyzed by |
GSE113533 |
