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 Type Contacts Ligation-free Multi-contact Enrichment Single-cell Public Experiment Sets Reference SOP
Dilution Hi-C DNA 119 Public Experiment Sets PMID:19815776
in situ Hi-C DNA 219 Public Experiment Sets PMID:25497547
single cell Hi-C DNA X 11 Public Experiment Sets PMID:24067610
sci-Hi-C DNA X 5 Public Experiment Sets PMID:28135255
sn-Hi-C DNA X 15 Public Experiment Sets PMID:28355183
DNase Hi-C DNA 21 Public Experiment Sets PMID:27685100
Micro-C DNA 7 Public Experiment Sets PMID:26119342
TCC DNA 7 Public Experiment Sets PMID:22198700
Capture Hi-C DNA biotinylated
29 Public Experiment Sets PMID:25938943
methyl Hi-C DNA Not yet ready for public release PMID:31384045
single cell methyl Hi-C DNA X Not yet ready for public release PMID:31384045
MC Hi-C DNA X Not yet ready for public release
MC-3C DNA X Not yet ready for public release
ChIA-PET DNA protein-IP 4 Public Experiment Sets PMID:28358394
PLAC-seq DNA protein-IP 8 Public Experiment Sets PMID:27886167
DNA SPRITE DNA X X 2 Public Experiment Sets PMID:29887377
RNA-DNA SPRITE RNA-DNA X X 1 Public Experiment Set PMID:29887377
MARGI RNA-DNA 2 Public Experiment Sets PMID:28132817
GAM DNA X X Not yet ready for public release PMID:28273065
TrAC-loop DNA X Not yet ready for public release PMID: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 Type Purpose Public Experiment Sets Reference SOP
2-stage Repli-seq Replication timing 64 Public Experiment Sets PMID:29599440
Multi-stage Repli-seq Replication timing Not yet ready for public release
ATAC-seq DNA accessibility 11 Public Experiment Sets PMID:24097267
TSA-seq DNA proximity to protein/structure 55 Public Experiment Sets PMID:30154186
DamID-seq DNA proximity to protein/structure 14 Public Experiment Sets PMID:17545983
ChIP-seq DNA binding/proximity to protein 56 Public Experiment Sets
NAD-seq DNA proximity to protein/structure 8 Public Experiment Sets PMID:31201210
CUT&RUN DNA binding/proximity to protein 61 Public Experiment Sets Protocol
TRIP Promoter activity 7 Public Experiment Sets PMID:23953119
Bru-seq RNA Quantification 1 Public Experiment Set PMID:23973811
RNA-seq RNA Quantification 36 Public Experiment Sets

  Imaging Experiments

Experiment Type Goal Modality Public Experiment Sets
SPT Molecule tracking Fluorescence Localization 68 Public Experiment Sets
Electron Tomography Structural mapping Electron Microscopy 3 Public Experiment Sets
Immunofluorescence Molecule Localization Fluorescence Localization 138 Public Experiment Sets
DNA FISH DNA localization Fluorescence Localization 275 Public Experiment Sets
RNA FISH RNA localization Fluorescence Localization 75 Public Experiment Sets