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Sample GSM813028 Query DataSets for GSM813028
Status Public on Nov 01, 2011
Title Duchenne Muscular Dystrophy sample 3 Replicate 2
Sample type RNA
 
Channel 1
Source name DMD
Organism Homo sapiens
Characteristics gender: Male
age (years): 11
muscle: Fascia lata tensor
Extracted molecule total RNA
Extraction protocol Normal and patient total RNA was purified using Trizol Reagent (Life technologies). Poly (A)+ RNA was purified from total RNA using oligo-dt linked oligotex resin (QIAGEN).
Label Cy5
Label protocol Cy3- and Cy5-labeled cDNA was prepared using the CyScribe cDNA post labeling Kit (Amersham Pharmacia Biotech). Samples from DMD and AGING patients were each labeled individually with Cy5. Reference patients were pooled and then labeled with Cy3.
 
Channel 2
Source name CONTROL
Organism Homo sapiens
Characteristics description: REFERENCE: pool of total RNA from 7 younger CONTROL muscle biopsies
gender: 5 Females / 2 Males
age (years): 14-30
muscle: Paravertebral
Extracted molecule total RNA
Extraction protocol Normal and patient total RNA was purified using Trizol Reagent (Life technologies). Poly (A)+ RNA was purified from total RNA using oligo-dt linked oligotex resin (QIAGEN).
Label Cy3
Label protocol Cy3- and Cy5-labeled cDNA was prepared using the CyScribe cDNA post labeling Kit (Amersham Pharmacia Biotech). Samples from DMD and AGING patients were each labeled individually with Cy5. Reference patients were pooled and then labeled with Cy3.
 
 
Hybridization protocol Microarrays were prehybridized for 1 hour at 42° C (in 10% BSA, 20XSSC, 10% SDS). 0.5 µg of labeled sample cDNA was mixed with 0.5 µg of labeled reference cDNA in 40 µl of hybridization mix (50X denhardt, 20XSSC, 10 µg/µl PolyA RNA, 10 µg/µl Yeast tRNA, 10% SDS, 50% formamide) and hybridized to the microarrays. Microarray hybridization was carried out overnight at 42° C in a humidified chamber. Finally, slides were washed and dried by centrifugation.
Scan protocol Array scanning was carried out using a GSI lumonics LITE dual confocal laser scanner with ScanArray Microarray Analysis Software. Raw scanner images were analyzed with Genepix Software (AXON LABORATORY).
Description DMD, Biological replicate 3 of 4, Technical replicate 2 of 2.
Data processing Data were normalized (LOWESS) and analyzed (data filtering) using the Micro-Array Data Suite of Computed Analysis (MADSCAN)
 
Submission date Oct 10, 2011
Last update date Nov 01, 2011
Contact name Daniel BARON
E-mail(s) daniel.baron@univ-nantes.fr
Organization name Institut national de la santé et de la recherche médicale-INSERM
Department UMR1064 - Centre de Recherche en Transplantation & Immunologie
Lab Tolerance et regulation lymphocytaire
Street address 30 Bd Jean Monnet
City Nantes
State/province Loire-Atlantique (44)
ZIP/Postal code 44093
Country France
 
Platform ID GPL14713
Series (1)
GSE32720 DMD vs. AGING

Data table header descriptions
ID_REF
VALUE normalized log2 ratio (Cy5/Cy3) representing test/reference

Data table
ID_REF VALUE
1 0.1608018
2 0.4585215
3 -0.2532731
4 0.2098378
5 -0.1205399
6 -0.04609421
7
8 -0.05569544
9 0.1934609
10 -0.326104
11 -0.03247644
12 0.1328018
13 0.01410813
14 -0.200068
15 -0.3778719
16 0.03030504
17 0.1646511
18
19 0.01973901
20 -0.02543835

Total number of rows: 17280

Table truncated, full table size 229 Kbytes.




Supplementary file Size Download File type/resource
GSM813028.gpr.gz 1.3 Mb (ftp)(http) GPR
Processed data included within Sample table

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