|
| Status |
Public on Jan 01, 2013 |
| Title |
Sarcoma Cell Line JNDSCRT |
| Sample type |
RNA |
| |
|
| Source name |
Gift from Dr. Jun Nishio, Department of Pathology, School of Medicine, Fukuoka University, Fukuoka, Japan.
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: tumour cell line
sarcoma and primary cell type: desmoplastic round cell tumor
other: Nishio et al., 2002
|
| Treatment protocol |
Undifferentiated human osteoblasts (HOB) were grown to 60% confluency in proliferation medium according to the manufacturer's (Clonetics) instructions. Differentiated HOB were grown for 21 days in differentiation mediua (Clonetics) and test samples were stained for Alakine Phosphatase, Alizarin S and Von Kossa staining to determine levels of differentiation. MSC were grown in adipogenic medium for 7 days.
|
| Growth protocol |
Primary cells and cell lines were grown accrding to standard protocols and used at passage 4-7.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Hgu133av2 GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix Scanner
|
| Description |
human sarcoma and primary mesenchymal cell lines
|
| Data processing |
For pre-processing of raw data (background correction, normalisation, and probeset summarisation) we used the Bioconductor affy package for the R prgramming language specifically the 'rma' algorithm
|
| |
|
| Submission date |
Jul 11, 2012 |
| Last update date |
Sep 01, 2016 |
| Contact name |
Stephen Henderson |
| E-mail(s) |
s.henderson@ucl.ac.uk
|
| Phone |
02076796827
|
| Fax |
02076796851
|
| Organization name |
UCL
|
| Department |
Cancer Institute
|
| Lab |
Viral Oncology
|
| Street address |
Paul O'Gorman Building, Huntley Street
|
| City |
London |
| ZIP/Postal code |
WC1E 6BT |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL96 |
| Series (1) |
| GSE39262 |
Human sarcoma cell lines and untransformed cells |
|
| Relations |
| Reanalyzed by |
GSE86363 |
