Experiment Types - Genomics and Imaging

  Genomics Experiments

HiGlass View
The largest category of genomics experiments are Chromatin Conformation Capture (3C) assays. In general these assays detect regions of the genome that are in close spatial proximity in the nucleus even though they may be separated by many kilobases in the linear chromosome DNA sequence or even reside on separate chromosomes. Many variations of this general approach have been developed :
  •  many recent ligation-based approaches perform the fixation, digestion and ligation in intact permeabilized nuclei
  • different classes of enzymes have been used in the digestion step
  • several ligation-free methodologies have been developed
  • while many methods detect pairwise interactions, several assays have been developed that can detect multiplexes of interacting DNA regions
  • some methods are designed to detect RNA-DNA contacts
  • several methods use immunoprecipitation (IP) of specific chromatin associated proteins or pull downs with targeted specific labeled nucleotide probes to enrich specific contactx.
 The types of 3C experiments for which data is available on the portal is summarized in the table below and includes links to the Datasets as well as the Experiment Type page, which in some cases includes additional description and information on uniform processing of that data type at the 4DN-DCIC. 3C datasets are usually visualized as 2-dimensional contact matrices - the majority of pages for 3C datasets contain HiGlass views of these matrices.

Chromatin Conformation Capture (3C) Experiment Types

Experiment TypeContactsLigation-freeMulti-contactEnrichmentSingle-cellPublic Experiment SetsReferenceSOP
Dilution Hi-CDNA 119 Public Experiment Sets PMID:19815776
in situ Hi-CDNA 219 Public Experiment Sets PMID:25497547
single cell Hi-CDNAX 11 Public Experiment Sets PMID:24067610
sci-Hi-CDNAX 5 Public Experiment Sets PMID:28135255
sn-Hi-CDNAX 15 Public Experiment Sets PMID:28355183
DNase Hi-CDNA 21 Public Experiment Sets PMID:27685100
Micro-CDNA 7 Public Experiment Sets PMID:26119342
TCCDNA 7 Public Experiment Sets PMID:22198700
Capture Hi-CDNAbiotinylated
29 Public Experiment Sets PMID:25938943
methyl Hi-CDNANot yet ready for public releasePMID:31384045
single cell methyl Hi-CDNAXNot yet ready for public releasePMID:31384045
MC Hi-CDNAXNot yet ready for public release
MC-3CDNAXNot yet ready for public release
ChIA-PETDNAprotein-IP 4 Public Experiment Sets PMID:28358394
PLAC-seqDNAprotein-IP 8 Public Experiment Sets PMID:27886167
DNA SPRITEDNAXX 2 Public Experiment Sets PMID:29887377
RNA-DNA SPRITERNA-DNAXX 1 Public Experiment Set PMID:29887377
MARGIRNA-DNA 2 Public Experiment Sets PMID:28132817
GAMDNAXXNot yet ready for public releasePMID:28273065
TrAC-loopDNAXNot yet ready for public releasePMID:30150754

In addtion to the 3C experiments 4DN also host other types of genomics data that can help elucidate the chromatin structure throughout the genome . Most of these data types can be visualized as one-dimensional tracks on a genome data browser. These 1D tracks can also be integrated into HiGlass views. The assay types and links to the corresponding datasets on the 4DN data portal are summarized below.

Other Genomics Experiment Types

Experiment TypePurposePublic Experiment SetsReferenceSOP
2-stage Repli-seqReplication timing 64 Public Experiment Sets PMID:29599440
Multi-stage Repli-seqReplication timingNot yet ready for public release
ATAC-seqDNA accessibility 11 Public Experiment Sets PMID:24097267
TSA-seqDNA proximity to protein/structure 55 Public Experiment Sets PMID:30154186
DamID-seqDNA proximity to protein/structure 14 Public Experiment Sets PMID:17545983
ChIP-seqDNA binding/proximity to protein 56 Public Experiment Sets
NAD-seqDNA proximity to protein/structure 8 Public Experiment Sets PMID:31201210
CUT&RUNDNA binding/proximity to protein 61 Public Experiment Sets Protocol
TRIPPromoter activity 7 Public Experiment Sets PMID:23953119
Bru-seqRNA Quantification 1 Public Experiment Set PMID:23973811
RNA-seqRNA Quantification 36 Public Experiment Sets

  Imaging Experiments

Experiment TypeGoalModalityPublic Experiment Sets
SPTMolecule trackingFluorescence Localization 101 Public Experiment Sets
Electron TomographyStructural mappingElectron Microscopy 3 Public Experiment Sets
ImmunofluorescenceMolecule LocalizationFluorescence Localization 138 Public Experiment Sets
DNA FISHDNA localizationFluorescence Localization 275 Public Experiment Sets
RNA FISHRNA localizationFluorescence Localization 77 Public Experiment Sets
Multiplexed FISHChromatin TracingFluorescence Localization 7 Public Experiment Sets
OptoDropletSynthetic CondensationFluorescence Localization 13 Public Experiment Sets