+This track holds the DANIO-CODE annotation of candidate regulatory elements, at five +developmental stages: Dome, 75% epiboly, 5-9 somites, Prim-5 and Long-pec. Four +related annotations are shown for each stage. +
+ ++ChromHMM is a segmentation of the whole genome into ten chromatin states. The +segmentation is learned from the combination of histone modifications present at each +position, and each state was then given a name by hand, using the Roadmap Epigenomics +annotation as a reference: active transcription start sites, their flanking regions, +active and primed enhancers, poised elements, Polycomb-repressed regions and a +quiescent state with no detectable mark. +
+ ++PADREs are predicted ATAC-supported developmental regulatory elements: the +subset of the segmentation that also lies in a region of open chromatin, which is the +consortium's set of candidate regulatory elements. Across all stages there are more +than 140,000 of them. cPADREs are the consensus set of 83,553 elements that are +called at every stage, so they can be compared position by position across +development. DOPEs are dynamic orphan predicted elements: regions that are open +at a given stage but carry no histone mark at all. +
+ ++This track is part of the DANIO-CODE collection. +
+ ++Each combination of annotation type and developmental stage is a separate track. On the +configuration page they are laid out as a grid, with the annotation type across and the +stage down. Only the ChromHMM tracks are checked when the grid is first opened. +
+ ++The ChromHMM and PADRE tracks are colored by chromatin state: +
+ +| + | 1_TssA1 — active transcription start site |
|---|---|
| + | 2_TssA2 — active transcription start site, second class |
| + | 3_TssFlank1 — region flanking a transcription start site |
| + | 4_TssFlank2 — region flanking a transcription start site, second class |
| + | 5_EnhA1 — active enhancer |
| + | 6_EnhFlank — region flanking an enhancer |
| + | 7_EnhWk1 — primed enhancer |
| + | 8_Pois — poised element |
| + | 9_ReprPC — Polycomb-repressed region |
| + | 10_Quies — quiescent, no mark detected |
+The DOPE tracks carry no state and are drawn in black. +
+ ++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. +
+ ++The genome was segmented with ChromHMM using the histone modification data in the +DC ChIP-seq track, and the ten resulting +states were named by comparison with the Roadmap Epigenomics annotation. Segments that +overlap an ATAC-seq peak were kept as PADREs. The PADREs were then classified further +by embedding their accessibility and histone signal with UMAP, which separates +promoters from enhancers and brings out subclasses that follow the timing of their +activity. Elements without any chromatin mark were split into those open at all stages +and those open only at some; the second group is shown here as DOPEs, and both groups +are shown pooled in the DC COPEs DOPEs +track. +
+ ++Element counts per stage, for PADREs: 85,750 at Dome, 93,394 at 75% epiboly, 123,324 +at 5-9 somites, 122,462 at Prim-5 and 148,870 at Long-pec. For DOPEs: 4,896, 5,862, +7,384, 7,699 and 6,468 for the same stages. The consensus cPADRE set has 83,553 +elements at every stage. +
+ ++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=dcComp. +
+ ++For automated download and analysis, the annotations are stored in bigBed files that +can be downloaded from +our +download server. Files are named after the stage and the annotation type, for example Prim5_PADREs.bb, Prim5_ChromHMM.bb, Prim5_cPADRE.bb and Prim5_DOPEs.bb. The stage names in the file names are Dome, Epi75, Hpf12, Prim5 and LongPec. 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/Prim5_PADREs.bb \ + -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 +
+