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Series GSE19694 Query DataSets for GSE19694
Status Public on Jul 23, 2010
Title Genome-wide analysis of siRNA accumulation in Arabidopsis treated with bacteria
Organism Arabidopsis thaliana
Experiment type Non-coding RNA profiling by high throughput sequencing
Summary To identify endogenous siRNAs in response to bacterial pathogen at a whole genome level, we performed small RNA profiling on Pseudomonas syringae-challenged Arabidopsis and obtained more than 24.6 million (M) reads with more than 3.8 M unique small RNAs that perfectly matched Arabidopsis genome. We found some new miRNAs and some miRNA induced by pathogen infection. We also identified more than 20K unique siRNAs from the NAT mRNAs and 22K siRNAs from the introns or intron-exon junction of the NATs.
Overall design Sequencing of small RNAs from Arabidopsis infected by control and 3 bacterias in 6h and 14h.
Contributor(s) Jin H, Chellappan P, Zhang W, Zhou X
Citation(s) 20696037, 20621980, 21153682
Submission date Dec 29, 2009
Last update date May 15, 2019
Contact name Weixiong Zhang
Phone 314-935-8788
Organization name Washington University in St. Louis
Department Computer Science and Engineering
Street address Campus Box 1045
City St. Louis
State/province MO
ZIP/Postal code 63130
Country USA
Platforms (1)
GPL9062 Illumina Genome Analyzer (Arabidopsis thaliana)
Samples (13)
GSM491567 mock_6hpi_rep1
GSM491568 mock_6hpi_rep2
GSM491569 hrcc_6hpi
SRA SRP001589
BioProject PRJNA122227

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE19694_RAW.tar 25.7 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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