Using next-generation sequencing, we sequenced transcriptomes of A. thaliana plants infected by the pathogenic and the symbiotic fungus and analyzed plant and fungal gene expression changes between pathogenic and symbiotic interactions. Infected plants were sampled at early infection stages, 12, 24, 48 and 96 HPI (hours post inoculation) Overall design: Infected plants were sampled at early infection stages, 12, 24, 48 and 96 HPI (hours post inoculation), and root tissues here fungal penetration and subsequent colonization take place were isolated for whole transcriptome sequencing (RNA-seq). Water-treated plants and auxenic fungal mycelia were used as control.