+A chromosome is not a straight line in the nucleus. It is folded so that some parts +touch each other far more often than others, and the regions of preferential contact +are called topologically associating domains. Domain boundaries matter for gene +regulation, because an enhancer usually acts on genes inside its own domain and rarely +across a boundary. Hi-C measures which parts of the genome are in contact by +crosslinking, cutting and religating chromatin, then sequencing the resulting pairs. +
+ ++This track does not show the contact matrix itself but two summary scores computed +from it along the genome. The insulation index is low where few contacts cross a +position, so its local minima mark domain boundaries. The directionality index +measures whether the contacts at a position point mostly upstream or mostly downstream, +and it flips sign at a boundary. Both are shown for 4 samples at 4 developmental stages +(256-cell, Dome, 75% epiboly and Prim-5) and at three window sizes, 50 kb, 500 kb and +1 Mb. +
+ ++This track is part of the DANIO-CODE collection. +
+ ++Each combination of sample, index type and window size is a separate auto-scaled graph. +Positive values are drawn in red and negative values in blue. The window size sets the +scale at which the index is computed, so the 50 kb tracks respond to local boundaries +and the 1 Mb tracks to large-scale compartments. +
+ ++Nothing is displayed until tracks are selected on the configuration page, where they +can be filtered by developmental stage, window size, index type and 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. +
+ ++The Hi-C data were processed by the group that produced them, and the insulation and +directionality indices were computed from the resulting contact matrices at 50 kb, +500 kb and 1 Mb windows. The samples come from the de Wit laboratory and were +originally deposited under GSE105015. +
+ ++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=dcHiC_Composite. +
+ ++For automated download and analysis, the annotations are stored in bigWig files that +can be downloaded from +our +download server. Files are named after the sample, the window size and the index type, for example DCD003008SQ_DCD017502DT_50000_di.bigWig for the directionality index at 50 kb and ..._ii.bigWig for the insulation index. Individual regions or the whole genome annotation can be +obtained using our tool bigWigToBedGraph, 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 +
+bigWigToBedGraph http://hgdownload.soe.ucsc.edu/gbdb/danRer11/danioCode/DCD003008SQ_DCD017502DT_50000_di.bigWig \ + -chrom=chr1 -start=20000000 -end=21000000 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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