|
| Status |
Public on Apr 18, 2017 |
| Title |
UM-Chor1_3 |
| Sample type |
RNA |
| |
|
| Source name |
Clivus chordoma_UM-Chor1
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Clivus chordoma
cell line: UM-Chor1
cell type: stable chordoma cell line
|
| Treatment protocol |
The cell lines were not treated with any reagents.
|
| Growth protocol |
The cell lines were cultured in Iscove’s Modified Dulbecco’s Medium/RPMI 1640 (4:1; Lonza, Basel, Switzerland) with 10 % fetal bovine serum (Biochrom AG, Berlin, Germany), 2 mM glutamine, and penicillin/streptomycin
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using the RNeasy Mini Kit (Qiagen) following the manufacturer's protocol. RNA was quantified using a NanoPhotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies).
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's protocol, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with a NanoPhotometer
|
| |
|
| Hybridization protocol |
100 ng of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s protocol. On completion of the fragmentation reaction, 25 µl of 2x Agilent HiRPM hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Human 4x44K Whole Genome Microarray (G412F) 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), 1 minute with 37°C GE Wash buffer 2 (Agilent) and 30 seconds with Acetonitril.
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent DNA microarray Scanner G2505B (5micron) with the the Agilent Scan Control Version A.8.4.1 .
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 12.0.1.1(Agilent) using Default Parameters (protocol GE1_1200_Jun14 and grid: 014850_D_F_20080627) to obtain Background subtracted and spatially detrended processed signal intensities.
|
| |
|
| Submission date |
Feb 20, 2017 |
| Last update date |
Apr 18, 2017 |
| Contact name |
Kevin Mellert |
| Organization name |
University Hospital Ulm
|
| Department |
Institute of Pathology
|
| Street address |
Albert-Einstein-Allee 23
|
| City |
Ulm |
| ZIP/Postal code |
89081 |
| Country |
Germany |
| |
|
| Platform ID |
GPL4133 |
| Series (1) |
| GSE95084 |
Characterization of chordoma cell lines derived from the clivus region |
|
