RNAseq RAW DATA of bacterial interactions with avocado roots

RNAseq comparing wt strain PcPCL1606 and the derivative mutant AdarB, defective in HPR production. RNA was extracted from the rhizosphere samples using a PowerSoil® RNA extraction kit (Qiagen Iberia S.L., Madrid, Spain) following the manufacturer's instructions and its amount was quantified using a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA). For the RNAseq experiment, the quantity and quality of RNA were verified by the Genomics and Ultrasequencing Service Unit (University of Malaga) and subsequently sequenced using NextSeq550 equipment (Illumina). The raw reads and their subsequent processing were carried out by the Centre for Supercomputing and Bioinnovation (University of Malaga). The bacterial RNAseq data analysis was performed based on a series of software packages adapted to the experimental model. The software components of the RNAseq analysis pipeline included analysis by SeqTrimNext (v.2.0.6) to remove low-quality reads, adapters, organular DNA and contaminant sequences; BOWTIE (v.2.2.9) to align reads to the genomic reference; Samtools (v. 0.1.19), a package of programs to deal directly with the alignment files, reading, writing, editing or viewing the alignment files in SAM/BAM format (http://www.htslib.org/); and TUXEDO tools (http://cole-trapnell-lab.github.io/cufflinks/manual/), used to estimate the aligned RNAseq reads in the different transcripts and estimate their abundance. The abundance of the transcripts was measured in fragments per kilobase of fragments of exon per million reads (fpkm). Once the transcripts and their corresponding estimated fpkm have been assembled, these transcripts were annotated with the known reference set of genes obtained from the database from the annotated reference file. This pipeline is a tool developed by the Andalusian Platform for Bioinformatics (PAB; http://www.scbi.uma.es/site/omics/bioinformatics) for the study of differential expression analysis using data of RNAseq on a genomic reference. The subsequent analysis of differential expression with a method analogous to differentially expressed sequences, and the graphical representation of the expression results was done using the 'cummeRbund' R package (v. 2.42.0). The array of reads in fpkm format generated will be used to obtain a list of differentially expressed genes that showed a p-value less than 0.05.NAseq comparing wt strain PcPCL1606 and the derivative mutant AdarB, defective in HPR production.