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Status |
Public on Jun 02, 2009 |
Title |
Stroma_Ras_0 Days 4OHT_rep2 |
Sample type |
RNA |
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Source name |
stroma, 0 days Ras activation, -4OHT
|
Organism |
Mus musculus |
Characteristics |
tissue: Mouse Stroma recipient strain: CB-17 scid/scid
|
Treatment protocol |
Tissue was excised and frozen immediately in OCT on dry ice and stored at -20C from weeks to months. Prior to LCM, tissue was sectioned (6um) and stored at -20C for up to 4 days. Sections were stained with cresyl-violet (LCM staining kit, Ambion) and immediately processed by laser capture microdissection. Slides were not allowed to sit more than 2.5 hours at room temp for processing.
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Growth protocol |
Epidermal tissue co-expressing ER:H-RasG12V and IkBaM was regenerated on female scid/scid mouse recipients. Grafts were allowed to heal for at least 3 weeks before Ras activation via daily i.p. injections of 730ug of 4OHT (in 110ul of a corn oil/ethanol mixture). Duplicate grafts were harvested after 0, 5, 20, and 35 days of 4OHT treatment.
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was extracted from laser capture microdissected tissue using RNAqueous kit following manufacturer's instruction (Ambion)
|
Label |
biotin
|
Label protocol |
Total RNA was amplified and fragmented using Message Amp II-Biotin following manufacturer's instruction (Ambion). 100-200ng of total RNA was amplified using 16 hr IVT reaction.
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Hybridization protocol |
Samples were hybridized by the Stanford P.A.N. facility using a Fluidics Station 450 and GeneChip Hybridization Oven 640 following manufacturer's instruction (GeneChip Expression Analysis Technical Manual Rev.2, Affymetrix). For the fluidics protocol, a Midi_euk2v3_450 script was used.
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Scan protocol |
Samples were scanned by the Stanford P.A.N. facility a on Affymetrix Scanner 3000 G7 (default target signal set at 500). Also, for the fluidics protocol, we used Midi_euk2v3_450.
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Description |
Adjacent Mouse Stroma Stroma_0Days_B
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Data processing |
The raw cel files were imported into GeneSpring 7 (Agilent) and RMA normalized. The only other normalization that was applied was setting values less than 0.01 to 0.01.
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Submission date |
Mar 19, 2009 |
Last update date |
May 14, 2009 |
Contact name |
Paul A Khavari |
Organization name |
Stanford University
|
Department |
Dermatology
|
Lab |
Khavari Lab
|
Street address |
259 Campus Dr
|
City |
Stanford |
State/province |
CA |
ZIP/Postal code |
94305-5168 |
Country |
USA |
|
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Platform ID |
GPL8321 |
Series (1) |
GSE15299 |
Modeling Inducible Human Tissue Neoplasia Identifies an ECM Interaction Network Involved in Cancer Progression |
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