|
| Status |
Public on Oct 05, 2005 |
| Title |
Gene expression profiling of MBC at 24 hours compared with MBN at 0 hour (A). |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
MBN0 (Reference)
|
| Organism |
Mus musculus |
| Characteristics |
C2C12 cell line; Tissue: muscle; Morphology: Myoblast; Properties: differentiation, muscle proteins express, myogenesis; Growing medium: DMEM + 2mM Glutamine + 10% Fetal Bovine Serum (FBS)
|
| Biomaterial provider |
Obtained from ATCC, USA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from myoblasts was purified following the standard Trizol standard protocol. The RNA 6000 LabChip kit (Agilent Technologies) was used for RNA quantification and quality control in conjunction with an Agilent Bioanalyzer 2001.
|
| Label |
Cy3
|
| Label protocol |
Total RNA , 15 ug, was retro-transcribed and directly labeled in the presence of Cy3 modified dCTP.
|
| |
|
| Channel 2 |
| Source name |
MBC24 (Test)
|
| Organism |
Mus musculus |
| Characteristics |
C2C12 cell incubated CAPAN-1 pancreatic cancer conditioned media for 24 hours.
|
| Biomaterial provider |
Obtained from ATCC, USA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from myoblasts was purified following the standard Trizol standard protocol. The RNA 6000 LabChip kit (Agilent Technologies) was used for RNA quantification and quality control in conjunction with an Agilent Bioanalyzer 2001.
|
| Label |
Cy5
|
| Label protocol |
Total RNA , 15 ug, was retro-transcribed and directly labeled in the presence of Cy5 modified dCTP.
|
| |
|
| |
| Hybridization protocol |
Microarray hybridisation was carried out in a dual slide chamber (HybChamber, Gene Machines, San Carlos, CA, USA) humidified with 100 µl of 3 x SSC. Labeled cDNA was dissolved in 40 µl of hybridisation buffer, denatured at 90°C for 2 min in a thermal cycler and applied directly to the slides. Microarrays were covered with 22 x 40 mm cover slip and hybridized overnight at 42°C by immersion in a high precision water bath (W28, Grant, Cambridge, UK). Post-hybridization washing was performed by serial incubations in buffers with decreasing SSC and SDS concentrations, at 42° C.
|
| Scan protocol |
Digital images were generated in a GSI Lumonics LITE dual confocal laser scanner (ScanArray Microarray Analysis Software) and processed with QuantArray Analysis Software (GSI Lumonics, Ottawa, Canada).
|
| Description |
Myoblasts were incubated with control (MBN) or CAPAN-1 pancreatic cancer conditioned media (MBC) for 0, 14 and 24 hours. RNAs purified from MBC at 14 and 24 hours were compared with RNA from MBN at 0 hour and at the corresponding stages. These samples were labeled and hybridized to muscle specific microarrays produced by our group (Human Array 2.0).
|
| Data processing |
The gene expression data analysis tool SNOMAD (http://pevsnerlab.kennedykrieger.org/snomadinput.html) was used for microarray data normalization and standardization. Log2 transformation was performed for each normalized expression value.
|
| |
|
| Submission date |
Oct 03, 2005 |
| Last update date |
Oct 04, 2005 |
| Contact name |
Gerolamo Lanfranchi |
| E-mail(s) |
stefano.cagnin@unipd.it
|
| Phone |
+39-0498276219
|
| Organization name |
University of Padova
|
| Department |
CRIBI - Biotechnology Center and Biology Department
|
| Lab |
Functional Genomics Lab
|
| Street address |
Via U. Bassi, 58/B
|
| City |
Padova |
| ZIP/Postal code |
35131 |
| Country |
Italy |
| |
|
| Platform ID |
GPL2011 |
| Series (1) |
| GSE3409 |
Gene expression profiling of pancreatic cancer cell conditioned myoblasts. |
|
