|
| Status |
Public on Mar 03, 2016 |
| Title |
DU145-shHIC1 |
| Sample type |
RNA |
| |
|
| Source name |
DU145-shHIC1
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: DU145
treatment: HIC1 silencing
|
| Growth protocol |
C4-2B cells were cultured in RPMI 1640 medium supplemented with 10% FBS (Invitrogen Corp, Carlsbad, CA). DU145 cells was cultured in DMEM medium with 10% FBS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA were extracted using Trizol (Invitrogen) following the manufacturer's recommendations. Total RNA was quantified by the NanoDrop ND-2000 (Thermo Scientific)and the RNA integrity was assessed using Agilent Bioanalyzer 2100 (Agilent Technologies).
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-2305) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
|
| |
|
| Hybridization protocol |
0.6 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Human Gene Expression Microarrays (G2505C) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 5 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then scan slides immediately to minimize the impact of environmental oxidants on signal intensities..
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent Human Gene Expression Microarrays (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100% (Hi) and 10% (Lo)).
|
| Data processing |
The scanned images were analyzed with Agilent Feature Extraction (FE) software using default parameters and set FE Project Properties to export data to txt.
|
| |
|
| Submission date |
Mar 02, 2016 |
| Last update date |
Apr 23, 2018 |
| Contact name |
Mingang Hao |
| E-mail(s) |
[email protected]
|
| Organization name |
Shanghai Jiao Tong University School of Medicine
|
| Department |
Department of Biochemistry and Molecular & Cell Biology
|
| Street address |
NO. 280 South Chongqing Road
|
| City |
Shanghai |
| ZIP/Postal code |
200025 |
| Country |
China |
| |
|
| Platform ID |
GPL17077 |
| Series (1) |
| GSE78850 |
Gene expression in human prostate cancer (PCa) cell lines upon HIC1 silencing |
|
| Relations |
| Reanalyzed by |
GSE113533 |
