Computational protocol: CXCL8 Chemokines in Teleost Fish: Two Lineages with Distinct Expression Profiles during Early Phases of Inflammation

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Protocol publication

[…] Carp CXCL8_L2 (GenBank accession number AB470924) and zebrafish CXCL8_L1_chr1 (GenBank accession number XM_001342570) sequences were used as query in BLAST searches. CXCL8_L1 genomic sequences were retrieved for zebrafish (Danio rerio), medaka (Oryzias latipes), tetraodon (Tetraodon nigroviridis), stickleback (Gasterosteus aculeatus) and fugu (Takifugu rubripes) from the EMSEMBL website (http://www.ensembl.org/index.html). CXCL8_L1 genes corresponded with Ensembl gene identifiers ENSTNIG00000017810 for tetraodon, ENSGACG00000001729 for stickleback, ENSORLG00000005096 for medaka and fugu Genbank accession number AB125645.1. BLAST searches against EST databases were performed on the website of NCBI (http://www.ncbi.nlm.nih.gov/). Zebrafish EST sequences corresponding to CXCL8_L2_chr17 were EH557944, EH536693, EH441857 and EH977746. Multiple sequence alignments were made with ClustalW within the MEGA4 software. Phylogeny trees were constructed with MEGA4 using Neighbour Joining (NJ; ) and Maximum Likelihood (ML; ). The online tool Genomicus (http://www.dyogen.ens.fr/genomicus-56.02/cgi-bin/search.pl) was employed to study conserved synteny for fish CXCL8 genes. Genomicus allows analysis of genes with approved gene symbols published on the ENSEMBL website. Since zebrafish CXCL8 genes are not yet annotated by ENSEMBL, annotated genes in close proximity to the genes of interest were used as reference genes in the analysis. Camk2d2 was taken as a reference gene for zebrafish CXCL8_L1_chr1, asb7 was used as a reference for zebrafish CXCL8_L2_chr7 and C14orf104/kintoun was used as a reference for zebrafish CXCL8_Chr17. […]

Pipeline specifications

Software tools Clustal W, MEGA
Databases Genomicus
Application Phylogenetics
Organisms Cyprinus carpio, Danio rerio, Homo sapiens