Unravelling Gene Regulation with the Dovetail Pan Promoter Panel

Advancements in genomics have revolutionized our understanding of gene regulation, paving the way for ground-breaking discoveries in various fields, from developmental biology to disease research. At the forefront of this transformative landscape is the Dovetail Pan Promoter Panel, a genomics tool designed to unravel the intricacies of gene regulation.
In this seminar, we invite you to embark on a journey into the world of regulatory genomics and explore the power of the Dovetail Pan Promoter Panel. Led by renowned experts in the field, this seminar will delve into the unparalleled capabilities of the panel and its potential to unlock the hidden secrets of gene expression.

Date: 30th August, 2023
Time:3:00 PM – 5:00 PM (Auckland, NZ)

Speaker 1: Professor Yasuhiro Murakawa
Kyoto University Institute for Advanced Study (KUIAS)
Dissecting human disease pathways using high-resolution chromatin contact maps
Large-scale genome-wide association studies (GWAS) have yielded an increasing number of disease-associated genomic loci. However, the functional interpretation still largely remains unclear. Recently, it has become apparent that disease-associated genetic variants are often found within enhancers. Enhances act to strongly enhance the expression of their target genes in a cell-type specific fashion, by physically associating with their promoters. We have developed a 5’-end single-cell RNA sequencing approach to comprehensively map active enhancers from heterogeneous helper T cells. By integrating with GWAS datasets, we identified hundreds of human enhancers associated with autoimmune diseases. To gain important clues to human disease pathways, here we used Micro-C as well as promoter-capture Micro-C, methods that can analyze chromatin interactions with super-high resolution. We systematically identified target genes of these enhancers, revealing novel human disease molecular mechanisms. In sum, we provide a general framework to investigate molecular mechanisms underlying human diseases.

Speaker 2: Myriam Elkhawand, Customer Success Manager, Dovetail Genomics
Setting up the Dovetail® Pan Promoter Assay in the lab
In this second talk, Myriam will delve into the details of Dovetail Pan Promoter protocol and library quality control measures that play a pivotal role in assessing the success of the assay. She will discuss best practices in carry out the assay, library QC, emphasizing the importance of stringent quality standards for reliable data analysis. She will also share the analysis pipeline for Dovetail Pan Promoter panels.

Pan Promoter Webinar_30 Aug

Nanopore Day, Queenstown 2023

Date: Thursday 31st August 2023
Venue: Queenstown, New Zealand
Time: 9:00 – 17:00

Hear about the latest technical updates for Oxford Nanopore Technologies as well as talks from local scientists about their latest work using nanopore technology.

There will also be an opportunity to submit questions throughout the talks, which will be answered in the Q&A sessions following each presentation.

Please note that this is an in-person event.

There is no delegate fee for this event, but registration is required at https://nanoporetech.com/event/NanoporeDayQueenstown

Your place at this event will be confirmed via email from events@nanoporetech.com.

Nanopore Day Queenstown_Flyer

Schedule available here: https://nanoporetech.com/event/NanoporeDayQueenstown

Join the Malacological Society of Australasia on September 7th, from 12 to 1:40pm (New Zealand time) for an enlightening open online symposium on molecular tools applied to molluscs! We will hear from AP Claudio González Wevar, AP Felipe Aguilera, and DP Hamish Spencer on the application of these tools to very different aspects of malacology. The symposium is free of change, just RSVP to receive a Zoom link. More information can be found on our website.

MSA_symposium

This online workshop is hosted by Genomics Aotearoa and NeSI and is for New Zealand researchers interested in progressing their skills with the R programming language.

This is an intermediate workshop, please check you meet the prerequisites: Attendees must have introductory knowledge of R and be well versed in tidyverse (Intro to R + supplementary materials in that workshop). We expect that you will either have completed our Introduction to R workshop or have sufficient experience of your own.

Some of the topics covered in the workshop are:

• Introduction to relational data and the join function.
• Working with regular expressions and functions from the stringr package.
• Writing custom functions, working with conditional statements.
• ‘Defensive programming’.
• Iterations – for loops, and map_*() functions.
• The importance of data structure in R.

Setup: This is a fully online, hands-on workshop. This workshop material will be run on the NeSI High Performance Computing (HPC) platforms – there is no need to install any software for this workshop. Instructions on how to access the NeSI HPC service will be sent out with the confirmation letter to registrants.

Participants must have their own laptops and plan to participate actively. You will require a working web browser.

This online workshop is hosted by Genomics Aotearoa and NeSI, and is for New Zealand researchers interested in progressing their abilities with Shell.

This workshop will include:

• An overview of the Shell, UNIX and Linux.
• Downloading data from a remote source and checking data integrity.
• Recap navigating files and directories, and commands used in routine tasks.
• Inspecting and manipulating data, part 1 (the head, less, grep, and sed commands).
• Inspecting and manipulating data, part 2 (using awk and bioawk to process text).
• Automating file processing.
• Challenges: solve example molecular biology problems using shell scripts.

This workshop assumes some familiarity with Shell. You will need to be able to do the following tasks via command line:

• Navigating files and directories.
• An understanding of full versus relative paths.
• Working with files and directories (examining files, creating, copying, moving and removing).
• Use a command line-based text editor such as nano.

And have a basic understanding of:

1. File/directory permission in Linux.
2. For loops (preferred, not required).

If you lack the above skills, you can use these sites as a refresher – Introduction to Command Line Carpentries lesson https://datacarpentry.org/shell-genomics/

Setup: This is a fully online, hands-on workshop. The workshop material will be run on the NeSI High Performance Computing (HPC) platforms – there is no need to install any software for this workshop. Instructions on how to access the NeSI HPC service will be sent out with the confirmation letter to registrants one week prior to the workshop.

You can view the workshop material, including the objectives and content, here: https://genomicsaotearoa.github.io/shell-for-bioinformatics/

Participants must have their own machine to work on and plan to participate actively in the workshop. You will require a working web browser.

Prof Kennerson is a Professor of Neurogenetics/Neurosciences with the ANZAC Research Institute, Sydney Local Health District (SLHD) and the School of Medical Sciences, University of Sydney, Australia. She heads the Translational Gene Discovery and Functional Genomics Inherited Peripheral Neuropathies Program at the ANZAC Research Institute. Her team has discovered several neuropathy genes and is doing pioneering research to investigate the role of structural variation and its role in new disease mechanisms for hereditary neuropathies. Her research program includes functional studies for recent gene (ATP7A and PDK3) and SV mutation (CMTX3 and DHMN1) discoveries using induced pluripotent stem cell derived motor neurons and animal models (C. elegans). Marina is a board member of the Charcot-Marie-Tooth and Related Neuropathies Consortium (CMTR), Chair of the Asian Oceanic Inherited Neuropathy Consortium (AOINC) serves on the Scientific Advisory Board of the CMT Research Foundation, USA and is Deputy Director (Research) of the SLHD Institute of Precision Medicine and Bioinformatics.

AEpiA-27 Sept[64]

We warmly invite you to attend our Genomics Aotearoa seminar, online on Friday, October 13 at 3pm.

We welcome Dr Gabriel Gasque (Head of Outreach, protocols.io) to talk about the power of sharing detailed methods – credit, preservation, and reproducibility.

Please invite colleagues to join our genomics community and take part in this seminar. Look forward to seeing you there. Questions and discussions are welcome.

Join from PC, Mac, iOS, or Android:
https://otago.zoom.us/j/97097442106?pwd=RlczU3VCdFBmbmt4Yng4VW5OcHdSdz09

About Gabriel
Dr Gabriel Gasque is an advocate of open science and experimental reproducibility and integrity. With more than 10 years of experience in the field, Gabriel is an expert in scientific dissemination, communication and publication.
Gabriel currently serves as Head of Outreach at protocols.io, a technology company whose goals are to foster scientific advancement through collaboration between researchers and promote transparency, reproducibility, integrity, and experimental accountability through the sharing and publication of detailed research protocols. Before joining protocols.io, Gabriel was a senior editor and team manager at PLOS Biology, the flagship journal of the Public Library of Science (PLOS).

Gabriel earned his PhD in Biochemistry from the National Autonomous University of Mexico (UNAM) and was awarded the Weizmann Prize from the Mexican Academy of Sciences for the best doctoral thesis in 2006. He conducted postdoctoral research at Columbia University and the Rockefeller University in the United States, as a Latin American PEW fellow.”

World-leading CRISPR-Cas researcher, Prof. Dr. Chase Beisel, is visiting the Department of Microbiology and Immunology on a Chaffer fellowship. He will be giving a seminar on October 15th from 1-2 pm in Biochemistry BIG13. Please see the attached flyer for details on this presentation.

2023_1016 Chase Beisel[42]