Open Access Highly Accessed Research article

RNA-seq liver transcriptome analysis reveals an activated MHC-I pathway and an inhibited MHC-II pathway at the early stage of vaccine immunization in zebrafish

Dahai Yang, Qin Liu*, Minjun Yang, Haizhen Wu, Qiyao Wang, Jingfan Xiao and Yuanxing Zhang*

Author Affiliations

State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China

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BMC Genomics 2012, 13:319  doi:10.1186/1471-2164-13-319

Published: 17 July 2012

Additional files

Additional file 1::

Solexa libraries of the WED immunized and PBS mock zebrafish liver. Six Solexa cDNA libraries were constructed from the livers of mock-immunized and WED-immunized zebrafish. Biological replicates (C1-C3 and V1-V3) were pooled to make representative samples for deep sequencing analysis. To assess the quality of sequencing, the reads were mapped to the zebrafish reference genome with no more than 5-mismatches. The sequencing data for C1-read 1 to C3-read 2 and V1-read 1 to V3-read 2 corresponded to the paired end sequencing (forward and reverse sequencing) data in each library, respectively.

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Additional file 2::

Annotation results of 4565 differentially expressed genes. Transcription level of each gene was deduced by determining the total number of reads mapped to each gene using Picard tools. Differentially expressed genes were identified by the DESeq package in R software using two-fold change (log2 (fold-change) ≥1 or ≤-1) and p-value <0.05 (cut-off at 5% false discovery rate (FDR)) as the threshold. “baseMean”, the base mean of counts divided by the size factors. “baseMean A”, the base mean for the counts of PBS-mock condition. “baseMean B”, the base mean for the counts of WED-immunized condition. “rpkm_avg_c”, the expression level of PBS-mock group. “rpkm_avg_v”, the expression level of WED-immunized group. “ZF-Annotation”, annotation of the differentially expressed genes through BLASTN similarity searches against the Ensembl zebrafish RefSeq mRNA database.

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Additional file 3::

GO function annotation results of 4565 differentially expressed genes. Functional enrichment for over- and under-expressed genes by more than two-fold in the WED-immunized group relative to the mock-immunized group generated by DAVID (v6.7). Gene functional enrichment was performed using the default parameters in DAVID to obtain an adjusted p-value <0.05 for the test gene group versus the zebrafish gene ontology (GO) annotation set. The fold-enrichment cut-off suggested by DAVID functional annotation was 1.5. The Biological Progress (BP-up and BP-down), Cellular Components (CC-up and CC-down), and Molecular Functions (MF-up and MF-down) associated with the GO analysis at different levels were also analyzed by BiNGO software. The hypergeometric test with Benjamini & Hochberg FDR were performed by the default parameters to obtain an adjusted p-value (<0.05) between the test gene group and the merged non-redundancy zebrafish (Danio rerio) and mouse (Mus musculus) GO annotation set.

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Additional file 4::

Primers for quantitative real-time PCR.

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