Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Xanthomonas campestris pv. Campestris 8004 far-red light irradiation and XccBphP overexpression transcriptional analysis

ABSTRACT: RNA isolation and RNA-Seq: Wild-type Xcc or pXccBphP strains were cultured in far-red light or dark conditions up to logarithmic phase (0.7 to 0.8 OD600) at 28C in PYM broth. Total bacterial RNA was isolated using the MasterPureTM RNA Purification Kit (Epicentre, Illumina). Samples corresponding to two biological replicates of each condition were submitted to Genome Qubec for rRNA removal with Ribo-Zero (Illumina) and TruSeq RNA-seq library preparation. 50 bp single-end sequencing of the libraries was performed using an Illumina HiSeq 2000 platform (Genome Qubec). Removal of low-quality reads and Illumina adapters, and assessment of the quality of the reads was performed using Trimmomatic (Bolger et al, 2014) and FastQC (www.bioinformatics.babraham.ac.uk/ projects/fastqc/), respectively. Rads were aligned to the Xcc genome obtained from GenBank (accession number: NC_007086.1) using SAMtools and the BurrowsWheeler Alignment software (BWA) (Li et al, 2009). Alignments were visualized using the software Integrated Genome Viewer (IGV) (http://broadinstitute.org/igv). RNA-Seq differential expression analysis: Read counts corresponding to annotated ORFs were quantified with the software FeatureCounts (Liao et al, 2014) using the strand specific mode. Differential expression analysis was performed using the software DESeq (Anders & Huber, 2010). Genes displaying adjusted p-value < 0.05.

INSTRUMENT(S): 0.7 W LED light, Illumina HiSeq 2000

ORGANISM(S): Xanthomonas campestris pv. campestris

SUBMITTER: Hernan Bonomi

PROVIDER: E-MTAB-4958 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Xanthomonas campestris attenuates virulence by sensing light through a bacteriophytochrome photoreceptor.

Bonomi Hernán R HR Toum Laila L Sycz Gabriela G Sieira Rodrigo R Toscani Andrés M AM Gudesblat Gustavo E GE Leskow Federico C FC Goldbaum Fernando A FA Vojnov Adrián A AA Malamud Florencia F

EMBO reports 20160912 11

Phytochromes constitute a major photoreceptor family found in plants, algae, fungi, and prokaryotes, including pathogens. Here, we report that Xanthomonas campestris pv. campestris (Xcc), the causal agent of black rot disease which affects cruciferous crops worldwide, codes for a functional bacteriophytochrome (XccBphP). XccBphP possesses an N-terminal PAS2-GAF-PHY photosensory domain triad and a C-terminal PAS9 domain as its output module. Our results show that illumination of Xcc, prior to pla ...[more]

PMID: 27621284

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Project description:Quantitative Analysis of cortical transcriptomes through Next Generation Sequencing (RNA-Seq) from wild-type mice, wild-type mice treated with IL1b (200 ng/mouse, 14h), IL-1R8-/- mice and IL-1R8-/- mice treated with IL1b antagonist Anakinra (25 mg/kg per day for 3 consecutive days, i.p. administration). mRNA profiles of cortical tissue from adult wild-type mice, wild-type mice treated with IL1b (200 ng/kg, 14h), IL-1R8-/- mice (Garlanda et al., 2004), and IL-1R8-/- mice treated with Anakinra (25 mg/kg per day for 3 consecutive days, i.p. administration) were generated by next-generation sequencing (RNA-seq) using Illumina HiSeq 2500 apparatus in paired-end configuration (2x125bp). Each condition was assessed in triplicate (12 mRNA-seq libraries) and, to reduce biological variability, each mRNA library was generated from pooled total RNA isolated from cortical tissue of 3 individual mice. In total, 9 mice per condition were used. Libraries were stranded and multiplexed. To increase sequencing depth, libraries were sequenced in two different lanes. All the libraries were loaded in each of the two lanes. Quality control of the raw data was performed with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Libraries were trimmed for adapter removal using Trimmomatic (Bolger et al., 2014) and mapped to reference genome (Ensembl GRCm38) using TopHat2 (Kim et al., 2013) and Bowtie2 (Langmead et al., 2009). Library sizes of primary mapped reads were between 70 and 96 million reads. Samtools was used to manipulate BAM files (Li et al., 2009). For calling of differentially expressed genes (DEG), mapped reads were counted with HTSeq v0.6.1 (Anders et al., 2014) and count tables were analysed using DeSeq2 v1.10.1 R-package (Love et al., 2014) with a design of one factor with four levels (“wild-type”, “wild-type + IL1”, “IL-1R8-/-”, “IL-1R8-/- + Anakinra"), and differences between groups were tested using contrasts for wild-type + IL1b versus wild-type; IL-1R8-/- versus wild-type; IL-1R8-/- + Kineret versus wild-type. For consideration of differentially regulated genes between conditions, we used adjusted p-value < 0.1 or adjusted p-value < 0.05 as indicated in the manuscript.

Dataset Information

Xanthomonas campestris pv. Campestris 8004 far-red light irradiation and XccBphP overexpression transcriptional analysis

Publications

Xanthomonas campestris attenuates virulence by sensing light through a bacteriophytochrome photoreceptor.

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