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Open Access Highly Accessed Research article

Deep sequencing-based transcriptome profiling analysis of bacteria-challenged Lateolabrax japonicus reveals insight into the immune-relevant genes in marine fish

Li-xin Xiang12, Ding He12, Wei-ren Dong12, Yi-wen Zhang12 and Jian-zhong Shao12*

Author Affiliations

1 College of Life Science, Zhejiang University, Hangzhou 310058, China

2 Key lab for Cell and Gene Engineering of Zhejiang province, Hangzhou 310058, China

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BMC Genomics 2010, 11:472  doi:10.1186/1471-2164-11-472

Published: 13 August 2010

Additional files

Additional file 1:

Table S1: Details on immune-relevant genes/homologues in L. japonicas.

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Additional file 2:

Table S2: Summary of tag mapping in DGE analysis for experimental and control groups.

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Additional file 3:

Figure S1: Tag abundance for mock- (A) and bacteria- (B) challenged group. Normalised tag copy number was calculated by dividing tag counts for each gene with the total number of tags generated for each library and are presented per one million transcripts. PM and 1 MM stand for perfect match and 1 miss match, respectively.

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Additional file 4:

Table S3: Summary of differentially expressed CD-containing consensus sequences.

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Additional file 5:

Table S4: Summary of putative novel immune/stress response consensus. Each consensus was analyzed using ProDom, SignalP, and TMHMM programs.

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Additional file 6:

Table S5: Primers used for validation analysis.

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Additional file 7:

Figure S2: Clustal W analysis for all IL-8-like CXC chemokines across all vertebrates.

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Additional file 8:

Figure S3: Phylogenetic analysis for all IL-8-like CXC chemokines across all vertebrates. A phylogenetic tree was constructed using the maximum likelihood method to show the relationship between L. japonicus IL-8 and other known vertebrate IL-8-like CXC-chemokines. Local bootstrap percentages were obtained after 10000 replications.

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