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Series GSE50085 Query DataSets for GSE50085
Status Public on Aug 22, 2016
Title Characterization and function of Tomato yellow leaf curl virus-derived small RNAs generated in the tolerant and susceptible tomato varieties using deep sequencing
Organism Solanum lycopersicum
Experiment type Non-coding RNA profiling by high throughput sequencing
Summary High-throughput sequence analysis of small RNAs of TYLCV-tolerant (containing tolerance gene Ty-1) and susceptible varieties indicated that miRNA-like vsRNAs and secondary vsiRNAs are mainly contributed to hotpots. Interestingly, various characteristics of vsRNAs among each sample are consistent, but in different number of expression; Deep sequencing of degradome provided evidence for the function of vsRNAs-mediated viral transcripts slicing; And bisulfite sequencing PCR suggested the geminivirus DNA methylation induced by vsRNAs. Comparison of the expression quantity and trend of viral DNA, mRNA and vsRNA inferred that the quantity of vsRNAs is significantly corresponding to the expression level of viral mRNA. Nevertheless, vsRNAs had finite effect on inhibition of virus replication and expression. Here, we also speculated that by RDR catalysis of vsRNAs amplification, the tolerance gene Ty-1 may take an effective inhibition of viral transcription at the beginning of TYLCV infection.
Overall design Examination of 6 different sRNA and 4 degradome library in 2 tomato material.
The main result of our paper is distinguish the host plant sRNA and viral-derived sRNA from the .fa files (MMS_21dpi, 30dpi and TY1S_21dpi, 30dpi).
Contributor(s) Xie BY, Bai M
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Submission date Aug 22, 2013
Last update date May 15, 2019
Contact name Miao Bai
Organization name Hunan Agricultural University
Street address Hunan Agricultural University, No. 1 Nongda Road, Furong
City Changsha
State/province Hunan
ZIP/Postal code 410128
Country China
Platforms (1)
GPL16345 Illumina HiSeq 2000 (Solanum lycopersicum)
Samples (10)
GSM1213982 MMC
GSM1213983 MMS_21dpi
GSM1213984 MMS_30dpi
BioProject PRJNA215996
SRA SRP029146

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE50085_RAW.tar 361.2 Mb (http)(custom) TAR (of FA)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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