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| Status |
Public on Dec 25, 2006 |
| Title |
Expression data from quadriceps muscle of young DMD patients and age matched controls |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
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| Summary |
Albeit increased serum CK level and abnormal muscle histology are always present, boys with DMD are phenotipically indistinguishable from the normal ones at birth and, in their first years of life, acquire early motor milestones at normal times. A clear defect in muscle function becomes generally apparent by the end of the second year. As the disease is typically diagnosed between the ages of 3 and 7, the first two years are often considered and referred to as clinically presymptomatic.
As a defined gene expression signature was shown to characterize these symptomatic patients we sought to investigate whether and to which extent alterations may be also present in muscle from presymptomatic DMD infants. To this aim, we used the Affymetrix technology to compare the individual expression profiles of 19 DMD patients with age at biopsy scattered along the first two years of the disease with those of 14 age matched controls. This approach allowed us to describe with high resolution the altered transcriptional state that characterizes this early, presymptomatic phase of the disease and highlight some molecular pathways as potential critical targets in the pathophysiology of the disease.
Keywords: two populations study
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| Overall design |
-Subjects
Relevant data about the participants are posted under supplementary material (Table ST1). All DMD patients (n=22) had diagnosis of Duchenne Muscular Dystrophy based on the absence of dystrophin immunoreactivity on quadriceps muscle sections. None of the participants at the time of biopsy was or had been under corticosteroid treatment. Control biopsies (n=14) were selected from diagnostic specimens which were not given a diagnosis of neuromuscular disease nor showed any non-specific myopathic signs. A MIAME compliant description of this study is posted under supplementary Material (MIAME compliance).
-RNA extraction.
Total RNA was extracted from frozen quadriceps muscle biopsies by TriZol. (TriZol reagent, Invitrogen). RNA was further purified using the RNAeasy mini kit following the RNA cleanup protocol as indicated by the manufacturer (QIAGEN). RNA purity and integrity was assessed by spectophotometric analysis and agarose gel electrophoresis.
-Affymetrix Genechips.
In this work we made use of one chip type: the affymetrix HG-U133A genechipCRNA synthesis was performed using 5ug of total RNA as template, as described in the Affymetrix Gene Expression Manual. Genechips were washed and stained in an Affymetrix fluidic station 430. To avoid overcorrelation, samples were processed 8 at the time and arranged to have both DMD and control samples in each experimental session.
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| Contributor(s) |
Pescatori M, Ricci E, Bernardini C, Tonali PA |
| Citation(s) |
17264171 |
| Submission date |
Oct 10, 2006 |
| Last update date |
Aug 10, 2018 |
| Contact name |
Mario Pescatori |
| E-mail(s) |
mariopescatori@gmail.com
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| Phone |
00393930761013
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| Organization name |
Health e-genomics
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| Street address |
Westplein 11
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| City |
rotterdam |
| ZIP/Postal code |
3016BM |
| Country |
Netherlands |
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| Platforms (1) |
| GPL96 |
[HG-U133A] Affymetrix Human Genome U133A Array |
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| Samples (37)
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| GSM139501 |
normal skeletal muscle, biological rep1 |
| GSM139502 |
normal skeletal muscle, biological rep2 |
| GSM139503 |
normal skeletal muscle, biological rep3 |
| GSM139504 |
normal skeletal muscle, biological rep4 |
| GSM139505 |
normal skeletal muscle, biological rep5 |
| GSM139506 |
normal skeletal muscle, biological rep6 |
| GSM139507 |
normal skeletal muscle, biological rep7 |
| GSM139508 |
normal skeletal muscle, biological rep8 |
| GSM139509 |
normal skeletal muscle, biological rep9 |
| GSM139510 |
normal skeletal muscle, biological rep10 |
| GSM139511 |
normal skeletal muscle, biological rep11 |
| GSM139512 |
normal skeletal muscle, biological rep12 |
| GSM139513 |
normal skeletal muscle, biological rep13 |
| GSM139514 |
normal skeletal muscle, biological rep14 |
| GSM139515 |
DMD skeletal muscle, biological rep1 |
| GSM139516 |
DMD skeletal muscle, biological rep2 |
| GSM139517 |
DMD skeletal muscle, biological rep3 |
| GSM139518 |
DMD skeletal muscle, technical rep1 |
| GSM139519 |
DMD skeletal muscle, biological rep4 |
| GSM139520 |
DMD skeletal muscle, biological rep5 |
| GSM139521 |
DMD skeletal muscle, biological rep6 |
| GSM139522 |
DMD skeletal muscle, biological rep7 |
| GSM139523 |
DMD skeletal muscle, biological rep8 |
| GSM139524 |
DMD skeletal muscle, biological rep9 |
| GSM139525 |
DMD skeletal muscle, biological rep10 |
| GSM139526 |
DMD skeletal muscle, biological rep11 |
| GSM139527 |
DMD skeletal muscle, biological rep12 |
| GSM139528 |
DMD skeletal muscle, biological rep13 |
| GSM139529 |
DMD skeletal muscle, biological rep14 |
| GSM139530 |
DMD skeletal muscle, biological rep15 |
| GSM139531 |
DMD skeletal muscle, biological rep16 |
| GSM139532 |
DMD skeletal muscle, biological rep17 |
| GSM139533 |
DMD skeletal muscle, biological rep18 |
| GSM139534 |
DMD skeletal muscle, biological rep19 |
| GSM139535 |
DMD skeletal muscle, biological rep20 |
| GSM139536 |
DMD skeletal muscle, biological rep21 |
| GSM139537 |
DMD skeletal muscle, biological rep22 |
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| Relations |
| BioProject |
PRJNA97809 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE6011_MIAME_compliance.pdf |
15.1 Kb |
(ftp)(http) |
PDF |
| GSE6011_Patient_data_(Table_ST1_).pdf |
33.4 Kb |
(ftp)(http) |
PDF |
| GSE6011_RAW.tar |
128.5 Mb |
(http)(custom) |
TAR (of CEL) |
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