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| Status |
Public on Feb 28, 2018 |
| Title |
Next Generation Sequencing Facilitates Quantitative Analysis of Murine Salivary Gland Transcriptomes |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular functions. The goal of this study is to compare NGS-derived salivary gland transcriptome profilings (RNA-seq) to better understand the molecular nature of the physiological differences in adult murine salivary glands.
Methods: Major murine salivary gland mRNA profiles were generated by deep sequencing, in triplicate, using Illumina HiSeq 2000. The sequence reads that passed quality filters were analyzed at the gene level with STAR followed by Cufflinks. In vivo NaCl reabsorption measurements were performed for validation.
Results: Using an optimized data analysis workflow, we mapped about 15 million sequence reads per sample to the mouse genome (build mm10) and identified 1991 genes that were differentially expressed across three major salivary glands. RNA-seq data provided valuable insights into the nature of the functional differences among the major salivary glands
Conclusions: Our study represents the first detailed analysis of murine salivary gland transcriptomes, with biologic replicates, generated by RNA-seq technology. Our results confirm functions of many genes, identified using genetically modified mice. We conclude that RNA-seq-based transcriptome characterization would offer a comprehensive and sensitive evaluation of the gene expression.
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| Overall design |
Salivary gland mRNA profiles of 12-week old mice were generated by deep sequencing, in triplicate, using Illumina HiSeq 2000.
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| Contributor(s) |
Melvin JE |
| Citation(s) |
29373073, 31833218 |
| |
| Submission date |
Mar 17, 2017 |
| Last update date |
Dec 31, 2019 |
| Contact name |
Catherine E. Ovitt |
| Organization name |
University of Rochester Medical Center
|
| Department |
Center for Oral Biology
|
| Street address |
601 Elmwood Ave, Box 611
|
| City |
Rochester |
| State/province |
NY |
| ZIP/Postal code |
14642 |
| Country |
USA |
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| Platforms (1) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
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| Samples (18)
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| Relations |
| BioProject |
PRJNA379545 |
| SRA |
SRP102060 |
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