|
| Status |
Public on Apr 18, 2018 |
| Title |
NPC_shEGFP_rep2 |
| Sample type |
RNA |
| |
|
| Source name |
Control NPCs for knockdown
|
| Organism |
Mus musculus |
| Characteristics |
cell type: In vitro differentiated neural progenitor cells
|
| Treatment protocol |
The transgene for shEGFP exprssion was introduced retrovirally.
|
| Growth protocol |
Neural progenitor cells were maintained on a gelatin-coated culture plate in a NPC medium consisting of RHB basal (StemCells) containing epidermal growth factor (EGF) (Peprotech) at 10 ng/ml and human basic fibroblast growth factor (bFGF) (Peprotech) at 10 ng/ml.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the RNeasy Mini Kit (Qiagen) and assessed by Agilent 2100 Bioanalyzer and the RNA 6000 LabChip Kit (Agilent Technologies).
|
| Label |
Cy3
|
| Label protocol |
Microarray experiments were performed according to the manufacturer’s instruction. Twenty hundred nanograms of total RNA was labelled with cyanine 3-CTP and hybridized in Whole Mouse Genome Microarray 4x44K G4122F (Agilent Technologies).
|
| |
|
| 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 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Microarray 4x44K G4122F for 17 hours at 65°C in a rotating 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 8×60 K array slides.
|
| Description |
Control NPCs for knockdown
|
| Data processing |
The array data were analyzed using GeneSpring software (Agilent). Gene expression values were normalized by excluding low-signal intensity data and percentile shifts.
|
| |
|
| Submission date |
Oct 25, 2017 |
| Last update date |
Apr 18, 2018 |
| Contact name |
Takashi Ikeda |
| E-mail(s) |
[email protected]
|
| Organization name |
Kyoto Univ.
|
| Street address |
53 Shogoin Kawahara-cho Sakyo-ku
|
| City |
Kyoto |
| ZIP/Postal code |
6068507 |
| Country |
Japan |
| |
|
| Platform ID |
GPL10787 |
| Series (2) |
| GSE89427 |
Srf destabilizes cell identity (Microarray_Agilent Technologies) |
| GSE90034 |
Srf destabilizes cell identity |
|
