|
| Status |
Public on Aug 16, 2016 |
| Title |
hiPS_SKOV3_rep1 |
| Sample type |
RNA |
| |
|
| Source name |
Cancer Stem Cell, induced from human iPS cell with culture medium of SKOV3, replicate 1
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Cancer Stem Cell, induced from human iPS cell with culture medium of SKOV3
gender: Female
age: 36
|
| Growth protocol |
Human iPS cells kept undifferentiated were cultured in induction medium to allow differentiation. During the induction of differentiation, half of the medium was exchanged every day and the cells were passaged once or twice every two weeks. The period of induction of differentiation was at least 28 days, and at most two months. The cells were cultured at 37 °C under the atmosphere of 2% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was prepared with the RNeasy column purification (QIAGEN) according to the manufacturer's instructions
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1ug Total RNA using the Low Input Quick Amp Labeling Kit(Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.
|
| |
|
| Hybridization protocol |
0.6ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE 8x60K Microarray Ver2.0 (Agilent) 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).
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).
|
| Description |
Gene expression of induced cancer stem cell established from human iPS cell with SKOV3 cell culture medium
OCC-hiPS-12
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.
Normalized signal intensity by Agilp in series supplementary file.
|
| |
|
| Submission date |
Jun 29, 2016 |
| Last update date |
Apr 23, 2018 |
| Contact name |
Akimasa Seno |
| Organization name |
Okayama University
|
| Department |
Applied Chemistry and Biotechnology
|
| Lab |
Nano-Biotechnology
|
| Street address |
1-1, Tsushima-Naka, 1-chome, Kita-Ku
|
| City |
Okayama |
| State/province |
Okayama |
| ZIP/Postal code |
7008530 |
| Country |
Japan |
| |
|
| Platform ID |
GPL17077 |
| Series (2) |
| GSE83880 |
Gene expression of developed cancer stem cells [OCC-hiPS] |
| GSE83883 |
Gene expression of developed cancer stem cells |
|
| Relations |
| Reanalyzed by |
GSE113533 |
