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Series GSE56094 Query DataSets for GSE56094
Status Public on Jun 02, 2015
Title Transcriptional dynamics driving MAMP-triggered immunity and pathogen effector-mediated immunosuppression in Arabidopsis leaves following infection with Pseudomonas syringae pv. tomato DC3000.
Organism Arabidopsis thaliana
Experiment type Expression profiling by array
Summary High-resolution temporal transcriptomic analysis of Arabidopsis thaliana leaves during infection by Pseudomonas syringae DC3000 and DC3000hrpA-thaliana
 
Overall design RNA was extracted from Arabidopsis leaves after mock-inoculation, infection with P. syringae DC3000 and infection with P. syringae DC3000hrpA-. 13 time points (0, 2, 3, 4, 6, 7, 8, 10, 11, 12, 14, 16, 17.5 hours post inoculation) were sampled from each treatment and four biological replicates (a single leaf) were harvested at each time point for each treatment. This led to 156 biological samples (13 time points x 3 treatments x 4 biological replicates). Four technical replicates of each biological sample were generated (624). The microarrays were two-channel CATMA arrays and hence two samples are hybridized to each array resulting in 312 arrays used in the experiment. A “loop design” was developed to enable efficient extraction of information about sample comparisons. Half the arrays were used to directly compare samples at different time points within the same treatment, and half directly compared the same time point and adjacent time points between treatments. This design maximizes the power of data comparisons over time and between treatments.
 
Contributor(s) Lewis LA, Polanski K, de Torres-Zabala M, Jayaraman S, Bowden L, Moore JD, Penfold CA, Jenkins DJ, Hill C, Baxter L, Kulasekaran S, Truman W, Littlejohn G, Pruskinska J, Mead A, Steinbrenner J, Hickman R, Rand D, Wild DL, Ott S, Buchanan-Wollaston V, Smirnoff N, Beynon J, Denby K, Grant M
Citation(s) 26566919, 26428397
Submission date Mar 21, 2014
Last update date Oct 08, 2019
Contact name Jonathan David Moore
E-mail(s) jonathan.moore@tgac.ac.uk
Organization name The Genome Analysis Centre
Department Platforms and Pipelines
Street address Norwich Research Park
City Norwich
ZIP/Postal code NR4 7UH
Country United Kingdom
 
Platforms (1)
GPL10840 CATMA Arabidopsis 30K V3 TAIR V9 spotted cDNA array
Samples (156)
GSM1354976 Mock 1 hours biorep A
GSM1354977 Mock 2 hours biorep A
GSM1354978 Mock 3 hours biorep A
Relations
BioProject PRJNA242405

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE56094_RAW.tar 995.7 Mb (http)(custom) TAR (of TXT)
Processed data included within Sample table

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