Day 1: Dovetail Seminar

Time: Tuesday, 12th May @ 22.00 Tokyo

Location: Zoom link will be posted in Slack

Part 1:  Proximity Ligation in Transcriptional Control, Chromatin Confirmation and Epigenetics Hierarchical three-dimensional (3D) topology, referred to as genome conformation or higher-order epigenetic features, heavily influences chromosomal structure and function. These 3D features can influence gene regulation by controlling the physical interactions between regulatory elements with their target genes. Chromatin conformation capture (3C) technologies are key tools in assessing higher-order epigenetic features. Here we introduce three new ways of investigating conformation through 3C technology:1) Omni-C - provides uniform genomic coverage that expands the utility of a Hi-C library to include WGS applications2) Dovetail Micro-C - generates a mononucleosome resolution of chromatin conformation3) Dovetail HiChIP - combines the targeted approach of ChIP-seq with Hi-C to describe protein-mediated chromatin interactions

Part 2: Omni-C: Restriction-enzyme free Hi-C in Genome Assembly

Restriction Enzyme (RE)-based Hi-C is blind to approximately 20% of mappable genomes due to low RE site density. Here we introduce Omni-C™ technology, a sequence-independent endonuclease-based proximity-ligation assay which addresses the limitations of RE-based Hi-C approaches.

This Seminar will highlight that Omni-C™ libraries uniquely contain proximity-ligation characteristics with the advantage of uniform genome-wide coverage. This expanded data type enables not only improved Genome Assemblies, but also applications relying on coverage uniformity, such as Structural Variation detection, SNP calling and phasing

 

Day 2: Dovetail Bioinformatics 101

Time: Wednesday, 13th May @ 22.00 Tokyo

Location: Zoom link will be posted in Slack

Jay Ghurye will address common open source tools to use with Omni-C data and proximity ligated datasets in general:

- Visualizing Hi-C data

- Loop Calling

- Phasing

- Genome Assembly

- Compartment/TAD calling

- Structural Variation

- Genotyping

- HiChIP and Capture-C

 

Day 3: Protocol Walkthrough

Time: Thursday, 14th May  @ 22.00 Tokyo

Location: Zoom link will be posted in Slack

- How to implement the 2-day Omni-C, Micro-C and HiChIP protocol in your lab

- What kind of input material can be used

- Low-input protocolUsing Capture-C with the Omni-C kit

- QCing proximity-ligated libraries

- Storage of material and safe stops in the protocol