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| Status |
Public on Nov 16, 2017 |
| Title |
Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and OsAFB6 overexpression mutant Transcriptomes |
| Organism |
Oryza sativa |
| 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. The goals of this study are to compare transgene-derived OsAFB6 overexpression mutant transcriptome profiling (RNA-seq) to microarray
Methods: young panicle(<1mm) mRNA profiles of 80 individual plants of OsAFB6 overexpression mutants and the correspondinng negative plants during the same transgenic event as control were generated by deep sequencing, in two replicate, using Illumina HiSeq 2000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks.
Results: Using an optimized data analysis workflow, we found 59 genes were upregulated and 229 genes were down regulated in OsAFB6 overexpression mutant.
Conclusions: Our study represents the first detailed analysis of young panicle transcriptomes of OsAFB6 overexpression mutant, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. 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 |
young panicle(<1mm) mRNA profiles of 80 individual plants of OsAFB6 overexpression mutants and the correspondinng negative plants during the same transgenic event were generated by deep sequencing, in two replicate,, using Illumina HiSeq 2000.
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| Contributor(s) |
He Q, Xing Y |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| BioProject |
PRJNA417348 |
| |
| Submission date |
Nov 15, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Qin He |
| E-mail(s) |
heqin327@163.com
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| Organization name |
National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research
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| Street address |
shizishan street
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| City |
Wuhan |
| ZIP/Postal code |
430070 |
| Country |
China |
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| Platforms (1) |
| GPL13160 |
Illumina HiSeq 2000 (Oryza sativa) |
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| Samples (4)
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