+A promoter is the region at which transcription of a gene begins. In vertebrates a +promoter rarely uses a single start base; it fires from a cluster of neighboring +positions, and which position dominates can change between developmental stages. CAGE +sequences the first bases of capped RNAs and therefore measures these start positions +directly. +
+ ++This track shows 28,142 consensus promoters, called by combining the CAGE tag clusters +of all DANIO-CODE samples into one set that is not tied to a single stage. It is +intended as a stage-independent reference set of promoter positions. The per-sample tag +clusters that go into it are in the DC +CAGE-seq track. +
+ ++This track is part of the DANIO-CODE collection. +
+ ++Promoters are drawn as blocks. The score reflects the CAGE expression supporting the +promoter. +
+ ++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 from all developmental stages were processed with the FANTOM pipeline, +tag clusters were called per sample, and the clusters were combined across samples into +a consensus set. +
+ ++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=dcConsensus_promoters. +
+ ++For automated download and analysis, the annotations are stored in bigBed files that +can be downloaded from +our +download server. The file is consens.canonical.danRer11.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/consens.canonical.danRer11.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 +
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