%0 Journal Article
%T The zebrafish transcriptome during early development
%A Liselotte Vesterlund
%A Hong Jiao
%A Per Unneberg
%A Outi Hovatta
%A Juha Kere
%J BMC Developmental Biology
%D 2011
%I BioMed Central
%R 10.1186/1471-213x-11-30
%X An average of 79 M total reads were detected from the different stages. Out of the total number of reads 65% - 73% reads were successfully mapped and 36% - 44% out of those were uniquely mapped. The total number of detected unique gene transcripts was 11187, of which 10096 were present at 1-cell stage. The largest number of common transcripts was observed between 1-cell stage and 16-cell stage. An enrichment of gene transcripts with molecular functions of DNA binding, protein folding and processing as well as metal ion binding was observed with progression of development. The sequence data (accession number ERP000635) is available at the European Nucleotide Archive.Clustering of expression profiles shows that a majority of the detected gene transcripts are present at steady levels, and thus a minority of the gene transcripts clusters as increasing or decreasing in expression over the four investigated developmental stages. The three earliest developmental stages were similar when comparing highly expressed genes, whereas the 50% epiboly stage differed from the other three stages in the identity of highly expressed genes, number of uniquely expressed genes and enrichment of GO molecular functions. Taken together, these observations indicate a major transition in gene regulation and transcriptional activity taking place between the 512-cell and 50% epiboly stages, in accordance with previous studies.Zebrafish (Danio rerio) is used as a model system in many different scientific fields due to its rapid development in combination with a relatively short generation time and ease of genetic manipulation [1-6]. However, the most prominent application of zebrafish has probably been within developmental biology. This is due to the ease with which the embryos are obtained, in addition to the transparency of the developing zebrafish embryo, which greatly aids observation of developmental processes.DNA sequencing has increased tremendously in throughput with the advent of next-g
%U http://www.biomedcentral.com/1471-213X/11/30