|
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 |