Transcriptomics

Dataset Information

14

Transcription profiling of soybean soybean line PI200492 resistant to P. pachyrhizi


ABSTRACT: Affymetrix soybean genome arrays were used to identify genes differentially expressed in the immune resistance response at 6, 12, 24, and 48 hours after inoculation with Phakopsora pachyrhizi isolates TW72-1 or HW94-1; soybean + HW94-1 = resistant; soybean + TW72-1 = susceptible Experiment Overall Design: For each of 4 time points (6, 12, 24 and 48 hours post inoculation) a soybean PI200492 plant was inoculated with 2 treatments: HW94-1, or TW72-1. A mock inoculation was performed and sampled at time 0. There were three biological replicates of the entire experiment, for a total of 27 samples. During data analysis two samples failed the quality control metrics and were removed from the analysis, leaving 25 samples in the final data set.

INSTRUMENT(S): 418 [Affymetrix]

ORGANISM(S): Glycine max  

SUBMITTER: katherine schneider  

PROVIDER: E-GEOD-8432 | ArrayExpress | 2008-06-16

SECONDARY ACCESSION(S): GSE8432PRJNA101495

REPOSITORIES: GEO, ArrayExpress

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Publications

A microarray analysis for differential gene expression in the soybean genome using Bioconductor and R.

Gregory Alvord W W   Roayaei Jean A JA   Quiñones Octavio A OA   Schneider Katherine T KT  

Briefings in bioinformatics 20070929 6


This article describes specific procedures for conducting quality assessment of Affymetrix GeneChip(R) soybean genome data and for performing analyses to determine differential gene expression using the open-source R programming environment in conjunction with the open-source Bioconductor software. We describe procedures for extracting those Affymetrix probe set IDs related specifically to the soybean genome on the Affymetrix soybean chip and demonstrate the use of exploratory plots including im  ...[more]

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