|
| Status |
Public on May 15, 2019 |
| Title |
TGF-β |
| Sample type |
RNA |
| |
|
| Source name |
TGF-β
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Tumor endothelial cell (TEC) -derived from melanoma
|
| Treatment protocol |
Tumor endothelial cells were cultured in the absence or presence of 1 ng/mL of TGF-β2 in combination with 50 ng/mL of FGF2 for 72 h.
|
| Growth protocol |
TEC were maintained in basal EGM-2MV medium (CC-3202, Lonza, Basel, Switzerland) containing 5% fetal bovine serum (FBS)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA fractions were prepared using Nucleo Spin (TaKaRaBio, Otsu, Japan) following the manufacturer's recommendations.
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions
|
| |
|
| Hybridization protocol |
1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml 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 SurePrint G3 Human GE 8x60K (G4851A) 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 (G2505C) 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 |
Dish culture
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-107) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
The file Second_array_normalized_data.txt includes raw, normalized values and detection flags.
|
| |
|
| Submission date |
Mar 29, 2019 |
| Last update date |
May 17, 2019 |
| Contact name |
Yasuhiro Yoshimatsu |
| E-mail(s) |
[email protected]
|
| Phone |
+81-3-5803-5449
|
| Organization name |
Tokyo Medical and Dental University
|
| Lab |
Department of Biochemistry
|
| Street address |
M&D tower N-707, 1-5-45 Yushima, Bunkyo-ku
|
| City |
Tokyo |
| ZIP/Postal code |
113-8549 |
| Country |
Japan |
| |
|
| Platform ID |
GPL21163 |
| Series (1) |
| GSE129048 |
FGF2-mediated regulation of TGF-β-induced endothelial-to-myofibroblast transition |
|
