|
| Status |
Public on Nov 10, 2011 |
| Title |
SMP_sarcoma_04 |
| Sample type |
RNA |
| |
|
| Source name |
GFP-positive fraction of sarcoma, SMP
|
| Organism |
Mus musculus |
| Characteristics |
strain: mixed B6.129 background
tissue: sarcoma
sarcoma cell-of-origin: skeletal muscle precursor cells (SMPs)
oncogenes: KRAS(G12V), p16p19null
gfp status: positive
|
| Treatment protocol |
Tumors were harvested, digested in DMEM + 0.2% collagenase type II (Invitrogen) + 0.05% dispase (Invitrogen) for 90 minutes at 37°C. Cells were suspended in HBSS with 2% FBS and 2mM EDTA containing 1μg/ml propidium iodide and 10μM calcein blue (Invitrogen) to identify the viable fraction of cells from which GFP-positive cells were isolated by FACS sorting. Cells were sorted twice to maximize purity.
|
| 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 from total RNA according to the standard Affymetrix protocol.
|
| |
|
| Hybridization protocol |
15ug of biotinylated cRNA were hybridized for 16hr at 45C to the Affymetrix GeneChip Mouse Genome 430 2.0 array. Following hybridization, arrays were washed and stained on the Affymetrix Fluidics Station 400.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
|
| Description |
Gene expression data from sarcomas of SMP origin.
|
| Data processing |
CEL files were imported into D-chip (version 1.0.0.1) and normalized in batch against an invariant set. Filtered probe sets were identified based on variation across samples being 1< standard deviation/Mean < 1000 with 50% of probes being present in array comparisons. Expression level cut offs were made at >600, >400 and >200, and expression being found in ≥ 50% of microarray samples.
|
| |
|
| Submission date |
Jul 08, 2010 |
| Last update date |
Nov 10, 2011 |
| Contact name |
Amy J Wagers |
| Organization name |
Joslin Diabetes Center
|
| Department |
Islet Cell and Regenerative Biology
|
| Lab |
Wagers lab
|
| Street address |
1 Joslin Place
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL1261 |
| Series (1) |
| GSE22841 |
Discrete subsets of myogenic and mesenchymal precursors give rise to soft tissue sarcomas of distinct lineage differentiation |
|
