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| Status |
Public on Nov 09, 2021 |
| Title |
Next Generation Sequencing Facilitates Quantitative Analysis of VSV-stimulated Wild Type and lncRNA-ISIR -/- spleen Transcriptomes |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways.
Methods: spleen mRNA profiles of 8-weeks-old WT and lncRNA-ISIR, used to be called lnRNA-IRF3, knockout mice were generated by deep sequencing, using BGISEQ-500 system.
The sequence reads that passed quality filters were analyzed at the transcriptional level with RSEM (RNA-seq by Expectation Maximization).
Conclusions: Our study represents the first detailed analysis of retinal transcriptomes, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.
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| Overall design |
spleen mRNA profiles of 8-weeks-old WT and lncRNA-ISIR-/- mice were generated by deep sequencing, using BGISEQ-500.
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| Contributor(s) |
Xu J, Cao X |
| Citation(s) |
34731629 |
| Submission date |
Oct 10, 2019 |
| Last update date |
Nov 11, 2021 |
| Contact name |
Junfang Xu |
| E-mail(s) |
xu1261251822@sina.com
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| Phone |
+8613916829034
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| Organization name |
national key laboratory of medical immunology
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| Street address |
800 Xiangyin Road
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| City |
Shanghai |
| ZIP/Postal code |
200433 |
| Country |
China |
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| Platforms (1) |
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| Samples (2) |
| GSM4116430 |
RNA-seq for transcriptome in WT spleen tissue |
| GSM4116431 |
RNA-seq for transcriptome in lnc-IRF3-/- spleen tissue |
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| Relations |
| BioProject |
PRJNA576864 |
| SRA |
SRP225065 |
