|
| Status |
Public on Dec 16, 2020 |
| Title |
HuCCT1_shBEX2-2_2 |
| Sample type |
RNA |
| |
|
| Source name |
HuCCT1 cells, transfected shBEX2-2 vector
|
| Organism |
Homo sapiens |
| Characteristics |
shRNA: BEX2 knock down
cell line: HuCCT1
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA from HuCCT1 cells was purified using RNeasy Mini Kits (Qiagen, Canada)
|
| Label |
Cy3
|
| Label protocol |
100 ng of total RNA was labeled using Low Input Quick Amp Labeling Kit
|
| |
|
| Hybridization protocol |
600 ng of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).
|
| Description |
BEX2-knock down cells
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (GE1_107_Sep09) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
|
| |
|
| Submission date |
Sep 03, 2019 |
| Last update date |
Dec 16, 2020 |
| Contact name |
Keiichi Tamai |
| E-mail(s) |
tamaikeiichi@med.tohoku.ac.jp
|
| Organization name |
Miyagi Cancer Center
|
| Street address |
1-47, Nodayama, Shiote, Medeshima
|
| City |
Natori, Miyagi |
| ZIP/Postal code |
981-1293 |
| Country |
Japan |
| |
|
| Platform ID |
GPL13607 |
| Series (1) |
| GSE136741 |
BEX2 suppresses mitochondrial activity and is required for dormant cancer stem cell maintenance in intrahepatic cholangiocarcinoma |
|
