Protocols: In each SAR experiment, at least 6 upper (2) leaves from 6 different plants pre-treated in 1 leaves with Psm (MgCl2) were pooled for one biological Psm- (mock-control) replicate. In this way, 3 biologically independent, replicate samples per treatment and plant genotype were obtained within each SAR set. Arabidopsis thaliana plants were grown individually in pots containing a mixture of soil, vermiculite and sand (8:1:1) in a controlled cultivation chamber with a 10-h day (9 AM to 7 PM; photon flux density 100 mol m-2 s-1) / 14-h night cycle and a relative humidity of 70 %. Day and night temperatures were set to 21C and 18C, respectively. Experiments were performed with 5- to 6-week-old, naive plants exhibiting a uniform appearance. To activate SAR, plants were infiltrated between 10 AM and 12 AM into three lower (1) leaves with suspensions of the bacterial pathogen Pseudomonas syringae pv. maculicola (OD600 = 0.005). Infiltration with 10 mM MgCl2 served as the mock-control treatment. Upper (2) leaves were harvested 48 h after the primary treatment for the determination of systemic gene expression by RNA-seq analyses. Three biologically independent, replicate SAR induction experiments were performed with Col-0 and sid2 plants. RNA was extracted from leaf sample replicates with the Plant RNeasy extraction kit (Qiagen, Germany), and treated on-column (Qiagen, Germany) and in solution with RNA-free DNAse (New England Biolabs, MA, USA). RNA integrity, sequencing library quality and fragment size were checked on a 2100 Bioanalyzer (Agilent, CA, USA). Libraries were prepared using the TruSeq RNA Sample Prep Kit v2 (Illumina, San Diego, CA) and library quantification was performed with a Qubit 2.0 (Invitrogen, Germany). Leaf samples were multiplexed 12 libraries per lane yielding approximately 150 million reads per lane.
ENA first public
2015-12-27
ENA last update
2015-12-17
External Id
SAMEA3716000
INSDC center alias
Institute for Molecular Ecophysiology of Plants, Department of Biology, Heinrich Heine University Dusseldorf
INSDC center name
Institute for Molecular Ecophysiology of Plants, Department of Biology, Heinrich Heine University Dusseldorf
INSDC first public
2015-12-27T17:02:19Z
INSDC last update
2015-12-17T12:40:51Z
INSDC status
public
Submitter Id
E-MTAB-4151:Sample 12_part 3
broker name
ArrayExpress
common name
thale cress
experimental set
1
genotype
sid2
replicate
C
sample name
E-MTAB-4151:Sample 12_part 3
stimulus
Pseudomonas syringae pv. maculicola