+This track is part of the DANIO-CODE track collection. A candidate enhancer predicted from chromatin data is a hypothesis until it is tested. The usual test in zebrafish is a transgenic reporter assay: the candidate sequence is placed in front of a minimal promoter driving a fluorescent protein, the construct is injected into embryos, and the embryos are examined for fluorescence. If the sequence is an enhancer, the fluorescence appears in a specific tissue at a specific stage.
This track shows 246 zebrafish enhancers that have been validated this way and that the DANIO-CODE consortium collected from the published literature into one curated catalogue. The consortium used them as an independent check on its own predictions, and they fall predominantly on elements that the chromatin data had classified as enhancers.
--This track is part of the DANIO-CODE collection. -
-Enhancers are drawn as blocks, in the colors stored in the data file.
The DANIO-CODE consortium assembled 1,802 zebrafish developmental genomics datasets, 1,438 of them already published and 366 generated by consortium members, and reprocessed all of them from the raw sequencing reads so that samples from different laboratories and different protocols can be compared with each other. ChIP-seq and ATAC-seq were run through the ENCODE pipelines, CAGE-seq through the FANTOM pipeline, and Hi-C and 4C-seq through the pipelines of the groups that produced them. The