+ChIP-seq finds the places in the genome where a particular protein sits. Chromatin is +crosslinked, sheared and pulled down with an antibody against the protein of interest, +and the DNA that comes with it is sequenced. For histone modifications the result is a +map of the chemical marks on the histones that DNA is wrapped around, and different +marks tend to sit at different kinds of element: H3K4me3 at active promoters, H3K4me1 +and H3K27ac at enhancers, H3K27me3 at genes that are silenced by Polycomb, and +H3K36me3 across the bodies of transcribed genes. For a transcription factor the result +is a map of its binding sites. +
+ ++This track shows ChIP-seq data for 104 zebrafish samples across 17 developmental +stages and 18 targets: the histone marks H3K4me3, H3K4me1, H3K27ac, H3K27me3, +H3K36me3, H3K14ac and the histone variant H2AFV; RNA polymerase II with two antibodies +(4H8 and 8WG16); and the transcription factors Pou5f3, Nanog, Sox10, Zic3, CTCF, Cdx4, +Sall4, Mxtx2 and Gata1. These are the data the consortium used to segment the genome +into chromatin states, which are shown in the +DC Elements track. +
+ ++This track is part of the DANIO-CODE collection. +
+ ++The track has two views that can be configured separately. Signal shows one +auto-scaled coverage graph per sample. Peaks shows the enriched regions called +from that signal, as blocks. +
+ ++Nothing is displayed until samples are selected on the configuration page, where they +can be filtered by ChIP-seq target, developmental stage and sample. There are more than +200 individual tracks, so select only the targets and stages you need. +
+ ++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. +
+ ++ChIP-seq libraries were mapped and peak-called with the ENCODE ChIP-seq pipeline. The +samples come from 10 laboratories, among them the Schier, Cairns, Bartel, Zon, +Horsfield, Driever, Skarmeta, Shkumatava, Mathavan and Mueller laboratories, and were +originally deposited under accessions including GSE32483, GSE41458, GSE44269, +GSE48254, GSE75356, GSE84602 and GSE95033. The accession of each sample is shown in +its track description line. +
+ ++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=dcChIPseqComposite. +
+ ++For automated download and analysis, the annotations are stored in bigWig and bigBed files that +can be downloaded from +our +download server. Files are named after the target and the DANIO-CODE sample accession, for example CTCF_DCD002910SQ_signal.bigWig and CTCF_DCD002910SQ_peak.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/CTCF_DCD002910SQ_peak.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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