|
| Status |
Public on Apr 04, 2013 |
| Title |
EWS-ATF1_48h_control |
| Sample type |
RNA |
| |
|
| Source name |
EWS-ATF1_48h_control
|
| Organism |
Mus musculus |
| Characteristics |
strain background: mixed background of C57/BL6, 129, and ICR
cell type: tumor cells
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNeasy Plus Mini kit
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop Spectrophotometer.
|
| |
|
| Hybridization protocol |
0.6 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 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.
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides.
|
| Description |
110323_NO11
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters 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 25, 2012 |
| Last update date |
Apr 05, 2013 |
| Contact name |
Yasuhiro Yamada |
| E-mail(s) |
yasu@ims.u-tokyo.ac.jp
|
| Organization name |
University of Tokyo
|
| Department |
Institute of Medical Science
|
| Lab |
Division of Stem Cell Pathology
|
| Street address |
4-6-1, Shirokanedai, Minato-ku
|
| City |
Tokyo |
| ZIP/Postal code |
108-8639 |
| Country |
Japan |
| |
|
| Platform ID |
GPL10787 |
| Series (2) |
| GSE41122 |
EWS/ATF1 activates Fos and induces soft tissue sarcomas from neural crest-derived cells [Agilent]. |
| GSE41123 |
EWS/ATF1 activates Fos and induces soft tissue sarcomas from neural crest-derived cells. |
|
