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| Status |
Public on Sep 14, 2017 |
| Title |
miRNA expression profiling of thymus samples from myasthenia gravis patients |
| Platform organism |
synthetic construct |
| Sample organism |
Homo sapiens |
| Experiment type |
Non-coding RNA profiling by array
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| Summary |
Autoimmune myasthenia gravis (MG) is characterized by thymic abnormalities such as hyperplasia and thymoma. Thymus plays an important role in self-tolerance and is involved in initiation and progression of the disease.
A large proportion of MG patient show the presence of ectopic germinal centers (GC) in thymus that are absent in normal individuals. However, the exact mechanism how this change in thymus morphology is triggered and if this is related to pathophysiology of the disease remains unknown.
In this study we have compared the mRNA profile of thymus samples obtained during a clinical trial (Thymectomy Trial in Non-Thymomatous Myasthenia Gravis Patients Receiving Prednisone Therapy. ClinicalTrials.gov Identifier: NCT00294658).
We have compared the miRNA profile of thymus samples that have distinct germinal centers with those that lack them using Affymetrix miRNA array 4.0 to identify the differentially expressed genes with in the two groups.
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| Overall design |
Sixteen frozen tissue samples collected during MGTX trial were cryo-sectioned and were stained with haematoxylin and eosin to examine morphological features and presence of germinal centers.
The H and E sections were evaluated by two blinded observers and graded depending on presence (Grades 1-4) or absence of germinal centers (Grade 0). Total RNA including small RNA was isolated from the remaining tissue using mirVana miRNA isolation kit.
The RNA samples were processed and applied to Affymetrix miRNA array 4.0. Array data was normalized, batch corrected and analyzed (1-way ANOVA) using Partek Genomics Suite program.
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| Contributor(s) |
Sengupta M, Wang B, Lee NH, Kusner LL, Kaminski HJ |
| Citation(s) |
30308012 |
| Submission date |
Sep 13, 2017 |
| Last update date |
Jul 25, 2021 |
| Contact name |
Manjistha Sengupta |
| Organization name |
George Washington University
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| Department |
Neurology
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| Street address |
2300 Eye Street NW, Ross Hall, Room #723
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| City |
Washington DC |
| State/province |
District of Columbia |
| ZIP/Postal code |
20037 |
| Country |
USA |
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| Platforms (1) |
| GPL21572 |
[miRNA-4] Affymetrix Multispecies miRNA-4 Array [ProbeSet ID version] |
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| Samples (16)
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| GSM2782266 |
Thymus sample 5, Grade 0 |
| GSM2782267 |
Thymus sample 6, Grade 0 |
| GSM2782268 |
Thymus sample 7, Grade 0 |
| GSM2782269 |
Thymus sample 8, Grade 1-4 |
| GSM2782270 |
Thymus sample 10, Grade 1-4 |
| GSM2782271 |
Thymus sample 11, Grade 0 |
| GSM2782272 |
Thymus sample 13, Grade 1-4 |
| GSM2782273 |
Thymus sample 15, Grade 0 |
| GSM2782274 |
Thymus sample 16, Grade 0 |
| GSM2782275 |
Thymus sample 17, Grade 0 |
| GSM2782276 |
Thymus sample 18, Grade 1-4 |
| GSM2782277 |
Thymus sample 19, Grade 0 |
| GSM2782278 |
Thymus sample 20, Grade 1-4 |
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| Relations |
| BioProject |
PRJNA407113 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE103812_RAW.tar |
14.7 Mb |
(http)(custom) |
TAR (of CEL, CHP) |
| Processed data included within Sample table |
| Processed data provided as supplementary file |
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