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| Status |
Public on Nov 01, 2014 |
| Title |
Differential expression of miRNAs in response to topping in tobacco roots |
| Organism |
Nicotiana tabacum |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
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| Summary |
Topping is an important cultivating measure for flue-cured tobacco, and many genes had been found to be differentially expressed in response to topping. But it is still unclear how these genes are regulated. MiRNAs play a critical role in post-transcriptional gene regulation, so we sequenced two sRNA libraries from tobacco roots before and after topping, with a view to exploring transcriptional differences in miRNAs.Two sRNA libraries were generated from tobacco roots before and after topping. Solexa high-throughput sequencing of tobacco small RNAs revealed a total of 12,104,207 and 11,292,018 reads representing 3,633,398 and 3,084,102 distinct sequences before and after topping. The expressions of 136 conserved miRNAs (belonging to 32 families) and 126 new miRNAs (belonging to 77 families) were determined. There were three major conserved miRNAs families (nta-miR156, nta-miR172 and nta-miR171) and two major new miRNAs families (nta-miRn2 and nta-miRn26). All of these identified miRNAs can be folded into characteristic miRNA stem-loop secondary hairpin structures, and qRT-PCR was adopted to validate and measure the expression of miRNAs. Putative targets were identified for 133 out of 136 conserved miRNAs and 126 new miRNAs. Of these miRNAs whose targets had been identified, the miRNAs which change markedly (>2 folds) belong to 53 families and their targets have different biological functions including development, response to stress, response to hormone, N metabolism, C metabolism, signal transduction, nucleic acid metabolism and other metabolism. Some interesting targets for miRNAs had been determined.
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| Overall design |
2 samples examined:roots before and after topping
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| Contributor(s) |
Weiqun L, Hongxiang G, Yunchao K |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
Nov 01, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
hongxiang guo |
| E-mail(s) |
guohongxiang06@126.com
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| Organization name |
henan agricultural university
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| Street address |
95 wenhua road
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| City |
zhengzhou |
| ZIP/Postal code |
450002 |
| Country |
China |
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| Platforms (1) |
| GPL13760 |
Illumina HiSeq 2000 (Nicotiana tabacum) |
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| Samples (2) |
| GSM825365 |
MiRNAs in tobacco roots before topping |
| GSM825366 |
MiRNAs in tobacco roots after topping |
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| Relations |
| SRA |
SRP009169 |
| BioProject |
PRJNA149009 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE33370_RAW.tar |
123.4 Mb |
(http)(custom) |
TAR (of FA, TXT) |
| GSE33370_Unique.fa.gz |
9.7 Kb |
(ftp)(http) |
FA |
| GSE33370_conserved_miRNAs.txt.gz |
2.7 Kb |
(ftp)(http) |
TXT |
| GSE33370_new_miRNAs.txt.gz |
3.9 Kb |
(ftp)(http) |
TXT |
| GSE33370_readme.txt |
562 b |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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