Differential expression analysis to aluminum toxicity in Citrus x limonia Osbeck

Here we deliver the Differential gene expression  on genes response to aluminum toxicity in Citrus x limonia. Root apices of ‘Mandarin’ lime plants grown for 60 days in nutrient solutions either with 1480 mM Al3+ or 0 mM Al3+ were analyzed by RNA-seq.

Clean reads were mapped to the sweet orange (Citrus sinensis) genome (Xu et al. 2013). Gene expression levels were calculated by CPM (Counts per million) reads. We used HTSeq ver. 0.6.1 (Anders et al. 2015) CPM estimation. The differentially expressed genes (DEGs) here reported by NOIseq ver. 2.16.0 (Tarazona et al. 2016). 

Results:

Number of differentially expressed (DE) features (Probability > 0.7): 3,351

Up-regulated (M > 0): 1,664
Down-regulated (M < 0): 1,687

All software were run on OmicsBox interface.

References:

Anders S., Pyl PT. and Huber W. (2015). HTSeq--a Python framework to work with high-throughput sequencing data. Bioinformatics (Oxford, England), 31(2), 166-9.

OmicsBox - Bioinformatics made easy. BioBam Bioinformatics (Version 2.0.36). March 3, 2019. www.biobam.com/omicsbox.

Tarazona S., Furio-Tari P., Turra D., Pietro AD., Nueda MJ., Ferrer A. and Conesa A. (2015). Data quality aware analysis of differential expression in RNA-seq with NOISeq R/Bioc package. Nucleic acids research, 43(21), e140.

Xu Q, Chen L-L, Ruan X, et al (2013) The draft genome of sweet orange (Citrus sinensis). Nat Genet 45:59–66.

Legend: 

Regulation - UP or DOWN = differentially expressed genes, UPregulated or DOWNregulated

Citrus_40_Al_2 -  Normalized CPM for root apexes under  1480 mM Al3+ 

Citrus_0_Al_1 - Normalized CPM for root apexes under  0 mM Al3+