|
| Status |
Public on Jun 16, 2006 |
| Title |
Gene expression profiling of FSHMD1A muscle (9a) |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
FSHMD1A deltoid muscle n°9(a)
|
| Organism |
Homo sapiens |
| Characteristics |
- Sex: M
- Age (years): 13
- EcoR1 Fragment length (Kb): 10
- Clinical severity: high
- Inflammation signs: minimal
- Regenerating fibres: none
- Ragged-red-fibres: none
- Myopatic features: minimal
|
| Biomaterial provider |
Muscle specimens were obtained from FSHMD1A patients examined at the Institute of Neurology of the Catholic University of Rome or at the Center for Neuromuscular diseases (U.I.L.D.M. Sezione Laziale), Rome.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using the TRIZOL reagent (Invitrogen/Life Technologies) and purified using RNeasy Mini Kit (Qiagen, Hilden, Germany).
|
| Label |
cy5
|
| Label protocol |
Linear amplification of mRNA was carried on using the Message-Amp-aRNA kit (Ambion, TX, USA) with two consecutive amplification steps, according to the manufacturer’s recommendations. Fluorescent cDNA targets were prepared by direct labelling 1.5 ug of aRNA from each sample.
|
| |
|
| Channel 2 |
| Source name |
normal deltoid control
|
| Organism |
Homo sapiens |
| Characteristics |
Pool of ten human deltoideous normal muscles
|
| Biomaterial provider |
Muscle specimens were obtained from subjects in whom a muscle disease was excluded by both clinical and histopathological criteria.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using the TRIZOL reagent (Invitrogen/Life Technologies) and purified using RNeasy Mini Kit (Qiagen, Hilden, Germany).
|
| Label |
cy3
|
| Label protocol |
Linear amplification of mRNA was carried on using the Message-Amp-aRNA kit (Ambion, TX, USA) with two consecutive amplification steps, according to the manufacturer’s recommendations. Fluorescent cDNA targets were prepared by direct labelling 1.5 ug of aRNA from each sample.
|
| |
|
| |
| Hybridization protocol |
Microarray hybridization was carried out in a dual slide chamber (HybChamber, Gene Machines, San Carlos, CA, USA) humidified with 100 ul of 3 x SSC. Labeled cDNA was dissolved in 40 ul of hybridization buffer, denatured at 90°C for 2 min and applied directly to the slides. Hybridization was performed overnight at 42°C by immersion in a water bath (W28, Grant, Cambridge, UK). The following post-hybridization washes were performed: 1XSSC, 0.1% SDS for 4 min at 42°C, 0,1X SSC, 0.1% SDS for 4 min at room temperature and 0,2X SSC for 2 min at room temperature.
|
| 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 |
We compared the transcription profiles of FSHMD1A deltoideous muscles with a pool of 10 human deltoideous muscles obtained from normal donors, in a microarray competitive hybridization.
|
| Data processing |
Normalized data were determined using the publicly available software MIDAS (TIGR Microarray Data Analysis System: http://www.tigr.org/softlab/). Normalized values (lowess normalization) were calculated for each spot, and converted in logarithmic scale. Final values correspond to log(2) ratio of the normalized intensities.
|
| |
|
| Submission date |
Jun 15, 2005 |
| Last update date |
Oct 28, 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) |
| GSE2820 |
Gene expression profiling in FSHMD1A muscle |
|
| Data table header descriptions |
| ID_REF |
|
| Array Row |
array row position in Human Array 2.0 |
| Array Column |
array column position in Human Array 2.0 |
| Row |
row probe position in sub-array |
| Column |
column probe position in sub-array |
| VALUE |
Log(2) ratio of normalized intensities, defined as Channel 1 divided by Channel 2 (test/reference) |
| ch1 Intensity |
Channel 1 median intensity |
| ch1 Background |
Channel 1 median local background |
| ch2 Intensity |
Channel 2 median intensity |
| ch2 Background |
Channel 2 median local background |
