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.
Chromatin Conformation Capture (3C) Experiment Types
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 |