|
| Status |
Public on Jun 08, 2009 |
| Title |
Gene expression profiling of SMA I patient (D) compared with age-matched normal muscle (Array B) |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Normal skeletal muscle (Reference)
|
| Organism |
Homo sapiens |
| Characteristics |
Biopsy of quadriceps femoralis normal skeletal muscles.
|
| Biomaterial provider |
Obtained from neuromuscular bank of tissues and DNA samples (Department of Neurosciences, University of Padova, Italy).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from biopsies 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, 1 μg, was retro-transcribed and labelled using the Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion) according to manufacturer's protocol.
|
| |
|
| Channel 2 |
| Source name |
SMAI patient D (Test)
|
| Organism |
Homo sapiens |
| Characteristics |
Biopsy of SMA I patient (D) quadriceps femoralis skeletal muscles.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from biopsies 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, 1 μg, was retro-transcribed and labelled using the Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion) according to manufacturer's protocol.
|
| |
|
| |
| Hybridization protocol |
Microarray hybridization was carried on overnight at 48°C by submerging microarrays closed in a sealed chamber (HybChamber, GeneMachines, San Carlos, CA, USA) in a high-precision water bath (W28 Grant, Cambridge, UK). Post-hybridization washing was performed according to the protocol suggested in the Amino Allyl kit.
|
| Scan protocol |
Fluorescence signals were detected by analyzing the microarrays in a Perkin-Elmer LITE dual confocal laser scanner guided by ScanArray Microarray Analysis Software, and raw microarray images were analyzed with QuantArray Analysis Software (GSI Lumonics, Ottawa, Canada).
|
| Description |
We performed microarray competitive hybridizations with RNA from muscle samples of single SMA I (Patient D) and age-matched muscle control. These samples were labeled and hybridized to muscle specific microarrays produced by our group (Human Array 2.0, GPL2011).
|
| Data processing |
Intensity values were processed with the gene expression data analysis tool MIDAS (www.tigr.org/software/tm4/). Normalized values were converted to a logarithmic scale.
|
| |
|
| Submission date |
Jul 02, 2007 |
| Last update date |
Jun 08, 2009 |
| 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) |
| GSE8359 |
Gene expression profiling in SMA I and III patients |
|
