CAGE (cap analysis of gene expression) sequences only the very first bases of capped RNA molecules. Each read therefore marks one transcription start site, at base resolution. Because promoters usually fire from a small cluster of neighboring start sites rather than a single base, the individual start sites are grouped into tag clusters, and a tag cluster is a good working definition of an active promoter.
This track shows CAGE data for 16 zebrafish samples spanning 12 developmental stages, from the 1-cell stage to the adult. Two kinds of data are shown: the raw signal, which is the number of transcription start sites seen at each base, and the tag clusters called from that signal. Zebrafish is a useful system for this because the promoters used by the mother's stored RNA and those used after the embryo's own genome switches on can sit within the same promoter region and are separable at this resolution.
This track is part of the DANIO-CODE collection.
The track has two views that can be configured separately. Signal shows one coverage graph per sample, auto-scaled to the window. Regions shows the tag clusters as blocks; the score of a cluster reflects its expression, and the colors are taken from the consortium's files.
Nothing is displayed until samples are selected on the configuration page, where they can be filtered by developmental stage and by sample.
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 pipelines are published at gitlab.com/danio-code, and samples were assigned to developmental stages using ZFIN and ENCODE nomenclature. See Baranasic et al. 2022 for details.
CAGE libraries were processed with the FANTOM CAGE pipeline. Tag clusters were called from the mapped start sites. The samples in this track come from the Mueller laboratory and were originally deposited under SRA055273.
At UCSC the tracks were converted from the consortium's public track hub at trackhub2.genereg.net/DANIO-CODE with the script danioCodeHubToRa.py, and the data files were copied from the same server. The data themselves were not modified. The steps are documented in our makeDoc.
The data can be explored interactively in table format with the Table Browser or the Data Integrator and exported from there to spreadsheet or tab-separated tables. From scripts, the data can be accessed through our API, track=dcCAGEseqComposite.
For automated download and analysis, the annotations are stored in bigWig and bigBed files that can be downloaded from our download server. Signal files are named after the DANIO-CODE sample accession, for example DCD001527SQ_signal.bigWig, and tag cluster files end in _tagCluster.bigBed. Individual regions or the whole genome annotation can be obtained using our tool bigBedToBed, which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found here. The tool can also be used to obtain features within a given range, for example
bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/danRer11/danioCode/DCD001527SQ_DCD011313DT_tagCluster.bigBed \
-chrom=chr1 -start=20000000 -end=20100000 stdout
The original data files, and the sample and protocol metadata behind them, are available from the DANIO-CODE data coordination center at danio-code.zfin.org and from the consortium's track hub at trackhub2.genereg.net/DANIO-CODE.
Thanks to the DANIO-CODE consortium for collecting, reprocessing and publishing these data, and to the laboratories that produced the original datasets.
Baranasic D, Hörtenhuber M, Balwierz PJ, Zehnder T, Mukarram AK, Nepal C, Várnai C, Hadzhiev Y, Jimenez-Gonzalez A, Li N et al. Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis- regulatory elements. Nat Genet. 2022 Jul;54(7):1037-1050. PMID: 35789323; PMC: PMC9279159