biomedical and healthCAre Data Discovery Index Ecosystem
biomedical and healthCAre Data Discovery Index Ecosystem
| Title: | Xanthomonas campestris pv. Campestris 8004 far-red light irradiation and XccBphP overexpression transcriptional analysis
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| dateReleased: |
12-03-2016
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| description: |
RNA isolation and RNA-Seq: Wild-type Xcc or pXccBphP strains were cultured in 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) (). 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.
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| privacy: |
not applicable
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| aggregation: |
instance of dataset
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| ID: |
E-MTAB-4958
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| refinement: |
raw
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| dateSubmitted: |
03-01-2016
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| keywords: |
functional genomics
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| dateModified: |
12-03-2016
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| availability: |
available
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| types: |
gene expression
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| name: |
Xanthomonas campestris pv. campestris
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| accessURL: | https://www.ebi.ac.uk/arrayexpress/files/E-MTAB-4958/E-MTAB-4958.raw.1.zip |
| storedIn: |
ArrayExpress
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| qualifier: |
gzip compressed
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| format: |
TXT
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| accessType: |
download
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| authentication: |
none
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| authorization: |
none
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| accessURL: | https://www.ebi.ac.uk/arrayexpress/files/E-MTAB-4958/E-MTAB-4958.processed.1.zip |
| storedIn: |
ArrayExpress
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| qualifier: |
gzip compressed
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| format: |
TXT
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| accessType: |
download
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| authentication: |
none
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| authorization: |
none
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| abbreviation: |
EBI
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| homePage: | http://www.ebi.ac.uk/ |
| ID: |
SCR:004727
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| name: |
European Bioinformatics Institute
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| homePage: | https://www.ebi.ac.uk/arrayexpress/ |
| ID: |
SCR:002964
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| name: |
ArrayExpress
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