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Sample GSM491576 Query DataSets for GSM491576
Status Public on Jul 23, 2010
Title ev_14hpi
Sample type SRA
 
Source name 4-week-old Col-0 WT Arabidopsis
Organism Arabidopsis thaliana
Characteristics tissue type: leaves
infection: Pst DC3000 carrying an empty vector (EV)
time point: 14h
Treatment protocol Leaves of 4-weekold Arabidopsis plants were infiltrated with Mock (10mM MgCl2), non-pathogenic strain Pst DC3000 hrc C, Pst DC3000 (EV) and Pst DC3000 (avrRpt2) at a concentration of 2 X 107 cfu/ml. The samples were collected at 6 and 14 hpi.
Growth protocol 4-week-old plants grown at 23°C with 12h light
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from infiltrated leaves and fractionated on 15% denaturing polyacrylamide gel. RNA molecules ranging from 18 to 26 nt was excised and ligated to 5’- and 3’-RNA adaptors using T4 RNA ligase followed by RT-PCR and gel purification as described in the Instruction from Illumina Inc. The small RNA libraries were sequenced by Illumina Inc and UCR core facility
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina Genome Analyzer
 
Description plants inoculated with (Pst) DC3000 EV for 14h
Data processing Raw sequence reads were parsed to remove the 3'-adaptor, and those reads that do not have the 3'-adaptor and contain N were removed. The processed files are named as "condition"_"time".uniq, where "condition" corresponds to mock or one of the 3 bacterial treatment (i.e., R2, hrcc, and ev), "time" indicates either 6 or 14hpi, and uniq means the files contain unique sequence reads with copy numbers. The first column in a processed file is the number of copies of the sequence listed in the second column.
 
Submission date Dec 29, 2009
Last update date May 15, 2019
Contact name Weixiong Zhang
E-mail(s) weixiong.zhang@wustl.edu
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
 
Platform ID GPL9062
Series (1)
GSE19694 Genome-wide analysis of siRNA accumulation in Arabidopsis treated with bacteria
Relations
SRA SRX015136
BioSample SAMN00007219

Supplementary file Size Download File type/resource
GSM491576_ev_14hpi_uniq.txt.gz 1.4 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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