|
| Status |
Public on Jan 01, 2018 |
| Title |
01_control |
| Sample type |
RNA |
| |
|
| Source name |
U87-control si
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Glioblastoma
cell type: U87MG astrocytic cells
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from U87 cells was extracted using NucleoSpin RNA (MACHEREY-NAGEL GmbH & Co. KG).
|
| 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, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
|
| |
|
| 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 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 by brief centrifugation.
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k 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 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
|
| |
|
| Submission date |
Oct 25, 2017 |
| Last update date |
Jan 23, 2018 |
| Contact name |
Takehiko Ueyama |
| E-mail(s) |
tueyama@kobe-u.ac.jp
|
| Phone |
+81-78-803-5962
|
| Organization name |
Kobe university
|
| Department |
Biosignal Research Center
|
| Lab |
Laboratory of Molecular Pharmacology
|
| Street address |
Rokkodai-cho 1-1, Nada-ku
|
| City |
Kobe |
| State/province |
Hyogo |
| ZIP/Postal code |
657-8501 |
| Country |
Japan |
| |
|
| Platform ID |
GPL20844 |
| Series (2) |
| GSE106142 |
Roles of Cdc42 and Rac in Bergmann glia during cerebellar corticogenesis (U87_CDC42RAC1-DKD) |
| GSE106143 |
Roles of Cdc42 and Rac in Bergmann glia during cerebellar corticogenesis |
|
