Unknown,Transcriptomics,Genomics,Proteomics

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Total RNA RNAseq from roots of Arabidopsis Col-0 and siz1-2, infected and non-infected with Heterodera schachtii

ABSTRACT: In this experiment we evaluate the transcriptional response to beet cyst nematode infection in wild-type (Col-0) and siz1 a knocked-down Arabidopsis thaliana (siz1-2). The data indicates that the mutation in siz1-2 leads to a strong transcriptional regulation in the plant, mostly of genes related to plant defense. The interaction of the mutation and infection by H. schachtii results in differential regulation of a small subset of genes. Samples were taken from whole root systems of mock or H. schahtii-infected 21 day-old seedlings (7 days post-infection). Each sample contained at least 18 plants and 3 biological replicates of each sample were collected.

INSTRUMENT(S): Maxwell 16 Instrument, NextSeq 500

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Mark Sterken

PROVIDER: E-MTAB-8193 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Background; Heterodera schachtii is an economically important plant parasitic nematode that forms a syncytium from a cell superficial to the formed vascular bundle by progressive recruitment of other cells into the structure. The pattern of plant gene expression changes dramatically inside the syncytium. The pathogen probably plays a major role in defining the plant response by choice of initial plant cell during precise behaviour in planta and/or by the secretions it releases. The modified plant cells enable a high feeding rate by the female nematode so enhancing its rate of development and subsequent daily egg production. Arabidopsis is widely used as a model plant to characterise molecular responses to nematodes (e.g. Sijmons et al., 1991 Plant J. 1:245-254.). A complete overview of the changes in plant gene expression when sedentary nematodes establish has not yet been gained using Arabidopsis or any other host plant. Experimental Approaches; Our initial studies will focus on the H. schachtii/Arabidopsis interaction. To assure reliable microarray screening care has been taken to minimise extraneous differences between samples (see "Growth conditions" section). At 21 days (Growth stage 3.2-3.5 Boyes et al., 2001 Plant Cell 13:1499-1510) Arabidopsis plants were challenged with rigorously sterilised, infective nematodes of H. schachtii as before (Urwin et al., (1997) Plant Journal 12: 455-461.). 35 sterile J2s were pipetted onto small ~0.5mm2 squares of sterile GF/A filter paper. The GF/A paper was left in direct contact with the zone of elongation on 3 lateral roots per plant for 48 hours. Control plants were mock inoculated with sterile water. Sections of root containing syncytia have been excised from the thin and transparent roots of Arabidopsis and collected into RNAlater solution (Ambion) at 21 days post infection (Growth Stage 6.1 Boyes et al. 2001). The female nematode has been removed with watch-maker's forceps. Equivalent sections of root have been harvested from non-infected plants. Material has been collected from c. 1000 plants for each of the two samples and the uninfected material serves as an internal control. Total RNA has been prepared from the reference and test root material using an RNeasy plant RNA preparation kit (Qiagen) according to methods required by GARNET.Some questions on the form are omitted as we are not using mutant or transgenic lines. This is our first application. Experimenter name = Peter Edward Urwin; Experimenter phone = 0113 343 3035/2909; Experimenter fax = 0113 343 3144; Experimenter address = Centre for Plant Science; Experimenter address = University of Leeds; Experimenter address = Leeds; Experimenter zip/postal_code = LS2 9JT; Experimenter country = UK Experiment Overall Design: 2 samples were used in this experiment

Dataset Information

Total RNA RNAseq from roots of Arabidopsis Col-0 and siz1-2, infected and non-infected with Heterodera schachtii

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