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| Status |
Public on Apr 02, 2020 |
| Title |
Assessment of Viral RNA in Idiopathic Pulmonary Fibrosis Using RNA-seq [nonPoly(A) RNA] |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Results: We identified sporadic low-level evidence of viral infections in our lung tissue specimens, but did not find a statistical difference for expression of any virus, including EBV, herpesvirus saimiri and HERV-K, between IPF and control lungs. To the best of our knowledge, this is the first publication that employs RNA-seq to assess whether viral infections are linked to the pathogenesis of IPF. Our results do not address the role of viral infection in acute exacerbations of IPF, however, this analysis patently did not support an association between herpes virus detection and IPF.
Conclusions: To the best of our knowledge, this is the first publication that employs RNA-seq to assess whether viral infections are linked to the pathogenesis of IPF. Our results do not address the role of viral infection in acute exacerbations of IPF, however, this analysis patently did not support an association between herpes virus detection and IPF.
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| Overall design |
We investigated the possible association between IPF and viral RNA expression using next-generation sequencing, which has the potential to provide a high degree of both sensitivity and specificity. We quantified viral RNA expression for 740 viruses in 28 IPF patient lung biopsy samples and 20 age-matched controls. Key RNA-seq results were confirmed using Real-time RT-PCR for select viruses (EBV, HCV, herpesvirus saimiri and HERV-K).
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| Contributor(s) |
Yin Q, Strong MJ, Zhuang Y, Flemington EK, Kaminski N, de Andrade JA, Lasky JA |
| Citation(s) |
32245461 |
| Submission date |
Oct 01, 2019 |
| Last update date |
Apr 13, 2020 |
| Contact name |
Qinyan Yin |
| E-mail(s) |
qyin@tulane.edu
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| Phone |
5049886918
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| Organization name |
Tulane University
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| Department |
Department of Medicine
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| Street address |
1430 Tulane Ave SL8509
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| City |
New Orleans |
| State/province |
Louisiana |
| ZIP/Postal code |
70112 |
| Country |
USA |
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| Platforms (1) |
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| Samples (17)
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| Relations |
| BioProject |
PRJNA575273 |
| SRA |
SRP223907 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE138283_chrHERV_KW_database_ver4.txt.count.xlsx |
42.4 Kb |
(ftp)(http) |
XLSX |
| GSE138283_chrvirus_human_virus_database_ver4.txt.count2.xlsx |
113.7 Kb |
(ftp)(http) |
XLSX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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