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Series GSE56117 Query DataSets for GSE56117
Status Public on Mar 22, 2017
Title Transcriptome Analysis of Arabidopsis thaliana and Changes of Glucosinolates Metabolism Pathway Induced by Flg22
Organism Arabidopsis thaliana
Experiment type Expression profiling by high throughput sequencing
Summary Purpose: The goals of this study are to analyze the transcriptome of Arabidopsis thaliana treated after flg22 and to find changes of glucosinolate metabolism genes after treatment.
Methods: Total mRNA of 10 day wild-type Arabidopsis seedlings that were treated with and without flg22( final concentrations 1μmol/L) in 1/2 MS medium for 4h, were extracted respectively. Each sample was harvested in three independent biological replicates with equal weight and mixed ,subsequently sequencing. The sequence reads that passed quality filters were mapped to the Arabidopsis_thaliana genome (TAIR10.18).Then the mapping genes were used for the abundance and functional analysis.
Results: We mapped about 45 million and 52 million sequence reads of control sample and treatment sample to the Arabidopsis_thaliana genome (TAIR10.18) and identified total 23,413 genes with Botiw/TopHat workflow. Comparison of the two samples showed 1,200 differentially expressed genes (DEGs), including 290 down-regulated and 910 up-regulated genes. The DEGs were associated with energy metabolism, amino acid metabolism and biosynthesis of secondary metabolites. After flg22 treatment, genes involved in indolic glucosinolate biosynthesis pathway were up-regulated significantly,which is further demonstrated by Real Time RT-PCR, while aliphatic glucosinolate pathway almost had no change, indicating the important role of indolic glucosinolates in plant defense responses.
Conclusion: Our study provides the overall genetic resource of Arabidopsis_thaliana after treated by flg22 to date. These data will pave the way for further studies about deeply understand pathogen induced defense and the contribution of indolic glucosinolates.
Overall design Two samples mRNA profiles of Arabidopsis thaliana seedlings treated and not treated by flg22 to final concentrations 1μmol/L for 4h ,were generated by deep sequencing, three biological replicates pooling together for each sample, using Illumina Hiseq 2000 platform.
Contributor(s) Yu X, Gao J, Li Y, Li J
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Submission date Mar 22, 2014
Last update date May 15, 2019
Contact name xinxin yu
Phone 13654680328
Organization name northeast agricultural university
Street address gongbin street
City Harbin
ZIP/Postal code 150000
Country China
Platforms (1)
GPL13222 Illumina HiSeq 2000 (Arabidopsis thaliana)
Samples (2)
GSM1356168 WT
GSM1356169 WT+flg22
BioProject PRJNA242476
SRA SRP040475

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Supplementary file Size Download File type/resource
GSE56117_processed_data_rpkm.txt.gz 1.3 Mb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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