|
| Status |
Public on Nov 02, 2009 |
| Title |
Liposarcoma_ALT_2_2 |
| Sample type |
RNA |
| |
|
| Source name |
Liposarcoma, Fresh Frozen
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Liposarcoma, Fresh Frozen
|
| Treatment protocol |
None
|
| Growth protocol |
Bone marrow hMSC were cultured in DMEM-LG plus Glutamax supplemented with 17% Hyclone FBS (Thermo Fisher Scientific, Waltham, MA) at 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Frozen Liposarcoma tissue was disrupted using a Hybaid Ribolyser at a setting of 5.5 for 5 x 10 second pulses with 30 second pauses in between and RNA was extracted using the RNeasy Lipid kit (Qiagen Inc, Hilden, Germany) as per manufacturers’ instructions. Primary hMSC aspirates were isolated by centrifugation at 700 g for 15 min at 4 °C over a Ficoll-Hypaque gradient (Sigma) and total RNA was extracted using Nucleospin II RNA extraction kit (Macherey-Nagel) as per manufacutor's instructions.
|
| Label |
Cy3
|
| Label protocol |
800 ng of total RNA was labelled with Cy3 using the Low RNA Input Linear Amplification Kit (Agilent technologies) as per manufacturor's instructions.
|
| |
|
| Hybridization protocol |
100ul of purified labelled total RNA was hybridised to Agilent 4x44K whole human genome arrays for 17 hours at 65C rotating at 10 rpm and washed as as per manufacturor's instructions for one colour arrays (Agilent Technologies).
|
| Scan protocol |
Slides were scanned using DNA microarray scanner model G2539A (Agilent Technologies) and Agilent Scan Control Software. Spot intensity and identity information was extracted using Agilent Feature Extraction Software.
|
| Data processing |
Normalised to the 75th percentile with intensities below 0.01 being set to 0.01. Data filtered to contain only those probes with Present, Marginal or Unknown status in 22 of 26 samples.
|
| |
|
| Submission date |
Jan 23, 2009 |
| Last update date |
Mar 23, 2012 |
| Contact name |
W. Nicol Keith |
| E-mail(s) |
n.keith@beatson.gla.ac.uk
|
| Organization name |
The University of Glasgow
|
| Street address |
Center for Oncology and Applied Pharmacology, University of Glasgow, CRUK Beatson Laboratories, Garscube Estate, Switchback Road
|
| City |
Glasgow |
| State/province |
Lanarkshire |
| ZIP/Postal code |
G61 1BD |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL6480 |
| Series (2) |
| GSE14529 |
A gene expression signature classifying telomerase and ALT immortalization II |
| GSE14533 |
A gene expression signature classifying telomerase and ALT immortalization |
|
