Comment[ArrayExpressAccession] E-GEOD-66300 MAGE-TAB Version 1.1 Public Release Date 2015-06-15 Investigation Title Analysis of WRKY33 binding sites and WRKY33-dependent gene expression in Arabidopsis thaliana upon Botrytis cinerea 2100 inoculation Comment[Submitted Name] Analysis of WRKY33 binding sites and WRKY33-dependent gene expression in Arabidopsis thaliana upon Botrytis cinerea 2100 inoculation Experiment Description This SuperSeries is composed of the SubSeries listed below. Refer to individual Series Term Source Name ArrayExpress EFO Term Source File http://www.ebi.ac.uk/arrayexpress/ http://www.ebi.ac.uk/efo/efo.owl Person Last Name Kracher Person First Name Barbara Person Email kracher@mpipz.mpg.de Person Affiliation Max Planck Institute for Plant Breeding Research Person Address Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, Cologne, Germany Person Roles submitter Protocol Name P-GSE66300-1 P-GSE66300-4 P-GSE66300-3 P-GSE66300-2 Protocol Description For inoculation of Arabidopsis plants the spores were diluted in Vogel buffer. 2.5x10 to the power of 5 spores mL-1 were used for spray inoculations of 4-week old intact plants. For mock treatment, Vogel buffer was used. Plants were kept prior to and during infection under sealed hoods at high humidity. Total RNA was extracted from mock treated (14 hpi) and B. cinerea inoculated (14 hpi) 4-week old plants (WT and wrky33) with using the RNeasy Plant Mini (Qiagen) according to the manufacturer’s instructions. mRNA sequencing libraries were constructed with barcodes using the TrueSeq RNA Sample Preparation Kit (Illumina). Lysates were clarified from sonicated nuclei and WRKY33-DNA complexes were isolated with an HA antibody. ChIP DNA was purified using a QIA quick PCR Purification kit (Qiagen) and subjected to a linear DNA amplification (LinDA) protocol (Shankaranarayanan et al., 2011) which included two rounds of ‘in vitro transcription’ by T7 RNA polymerase. The resulting LinDA DNA was used to generate sequencing libraries bearing barcodes using a NEBNext ChIP-Seq Library Pre Reagent Set for Illumina kit (New England Biolabs). Arabidopsis Col-0 plants were grown for 4 weeks under short-day conditions in closed cabinets (Schneijder chambers: 16 h light/ 8 h dark cycle at 22-24°C, 60% relative humidity) on 42mm Jiffy-7 pots (Jiffy) to prevent contaminations from garden soil. Before sewing, the Jiffy pot peat pellets were re-hydrated in water containing 0.1% liquid fertilizer Wuxal (Manna). B. cinerea strain 2100 was cultivated on potato dextrose plates at 22°C for 10 days. Spores were collected, washed, and frozen at -80C in 0.8% NaCl at a concentration of 10 to the power of 7 spores mL-1. Protocol Type sample treatment protocol nucleic acid library construction protocol nucleic acid library construction protocol growth protocol Experimental Factor Name treatment chip antibody genotype Experimental Factor Type treatment chip antibody genotype Comment[SecondaryAccession] GSE66300 Comment[GEOReleaseDate] 2015-06-15 Comment[ArrayExpressSubmissionDate] 2015-02-25 Comment[GEOLastUpdateDate] 2015-06-16 Comment[AEExperimentType] RNA-seq of coding RNA Comment[AEExperimentType] ChIP-seq SDRF File E-GEOD-66300.sdrf.txt