|
| Status |
Public on Apr 28, 2015 |
| Title |
MCF7GLI1 |
| Sample type |
RNA |
| |
|
| Source name |
MCF-7 expressing GLI1.
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: MCF-7
genotype/variation: expressing GLI1
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Not provided.
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the One-Color Low RNA Input Quick Amplification 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 ND-1000 Spectrophotometer.
|
| |
|
| Hybridization protocol |
0.6 ug 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 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 v2 8x60K Microarray (G4851B) 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 10um, Dye channel is set to Green and Green PMT is set to 100%).
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 039494_D_F_20120628) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
|
| |
|
| Submission date |
Dec 19, 2014 |
| Last update date |
Apr 23, 2018 |
| Contact name |
Kenji Kasai |
| E-mail(s) |
[email protected]
|
| Organization name |
Aichi Medical University School of Medicine
|
| Department |
Department of Pathology
|
| Street address |
1-1 Yazakokarimata
|
| City |
Nagakute |
| State/province |
Aichi |
| ZIP/Postal code |
480-1195 |
| Country |
Japan |
| |
|
| Platform ID |
GPL17077 |
| Series (1) |
| GSE64350 |
GLI1-regulated genes in human mammary epithelial cells and human breast cancer cells |
|
| Relations |
| Reanalyzed by |
GSE113533 |
