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| Status |
Public on Jan 01, 2017 |
| Title |
Analysis of alternatively spliced transcripts in leaf, root, panicle and seed of rice with a long oligomer microarray |
| Organism |
Oryza sativa |
| Experiment type |
Expression profiling by array
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| Summary |
RNA splicing is a molecular mechanism to increase protein diversities acquired through the evolution while the underlieing driving forces for the phenomenon are unknown especially in terms of gene expression. Rice alternatively spliced transcript detecting microarray (ASDM) was designed and applied to differentiate the transcriptome of 4 representative organs of Oryza sativa L. cv. Ilmi including leaves, roots, panicles at 1 cm stage and young seeds at 20 days after pollination. The comparison of the data between the microarray and RNA-seq shows a ‘bell shape distribution’ and a strong co-lineation for highly expressed genes. The transcripts are classified according to the degree of organ enrichment using coefficient value (CV, the ratio of standard deviation to the mean values); highly variable (CVI), variable (CVII), and constitutive (CVIII) groups. The genes of highly variable group show the characteristics of the organs. The index of the portion of loci with alternatively spliced transcripts in a group (IAS) is designated for these CV groups and showed the higher value in the constitutive group. In addition, within a locus, a transcript with longer cds tends to be higher expressed and the spliced_intron is the most commonly found type of alternative splicing for the extended cds. Thus, constitutively expressed genes might be under evolutionary pressure toward alternative splicing that might have a longer cds. These data show that less resource consuming and better designed microarray might be a niche technology to test the transcriptome analysis including alternatively spliced transcripts in plants.
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| Overall design |
We applied rice ASDM to detect organ specific genes among leaf, root, young flower at panicle 1 cm (P1cm) and seed at 20-30 days after pollination (S21DAP).
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| Contributor(s) |
Chae S, Nahm B, Kim Y |
| Citation missing |
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| Submission date |
Sep 30, 2016 |
| Last update date |
Jan 03, 2017 |
| Contact name |
Yeon-Ki Kim |
| E-mail(s) |
kim750a11@gmail.com
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| Phone |
82-31-321-6351
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| Organization name |
GreenGene Biotech Inc.
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| Department |
GreenGene Biotech Inc.
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| Lab |
Genomics & Genetics Ins.
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| Street address |
38-2 Namdong
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| City |
Yongin |
| State/province |
Kyonggido |
| ZIP/Postal code |
449-728 |
| Country |
South Korea |
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| Platforms (1) |
| GPL22515 |
Agilent-074336 Oryza sativa alternatively spliced transcript detecting microarray (OsASDM1, version 1) |
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| Samples (8)
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| Relations |
| BioProject |
PRJNA345049 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE87536_RAW.tar |
67.8 Mb |
(http)(custom) |
TAR (of TXT) |
| Processed data included within Sample table |
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