Digitized Course Information

Course information and metadata

This course has been released as an Open Educational Resource. Below you can find the metadata, including access & reuse information.

Description

Title: Biodiversity Genomics Europe and SciLifeLab Hi-C Course
Description: A course aiming to provide open, sustainable training in laboratory preparation of Hi-C libraries for reference genome sequencing of non-model organisms for BGE partner sequencing centers.
Authors: Maria Laura Aguilera Gil4 , Lorenzo Ballini8 , Laurie Bertrand3 , Simona Buonanno7, Eunkyong Choi6 , Annunziata De Luisi7, Giada Ferrari9 , Leonardo Girlanda8 , Carmela Gissi7 , Maria Gyftea6, Brian Kilburn1, Karine Labadie3 , Tuuli Lundback-Lärva6 , Graeme Oatley5 , Fernando Cruz Rodriguez4 , Irene Fabiola Roman Maldonado5 , Lily Shiue2 , Morten Skage9 , Pamela Veneziano Broccia4 , Ave Tooming-Klunderud9 , Olga Vinnere Pettersson6

1 Arima Genomics (US)
2 Cantata Bio (UK)
3 Genoscope (FR)
4 National Center for Genomic Analysis (ES)
5 Sanger Institute (UK)
6 SciLifeLab (SE)
7 University of Bari Aldo Moro (IT)
8 University of Florence (IT)
9 University of Oslo (NO)
Author contact details: olga.pettersson@igp.uu.se
Contributors: Kristen Schroeder1 , Jill Jaworski1 , Hampus Pehrsson Ternström1
1 SciLifeLab (SE)
Type: Video
Language: English
Keywords: Hi-C, genomics, biodiversity, sequencing
Content provider: SciLifeLab and Biodiversity Genomics Europe consortium
Date created: June 9-14, 2024
Date published: August 31, 2025

Educational

Learning outcomes: By the end of the course, participants will be able to:

  • independently prepare HiC libraries of low-complexity samples.
  • prepare HiC libraries at their home labs.
  • understand the most crucial steps of the protocol
  • troubleshoot crucial steps of the protocol in their home labs when applied to high-complexity samples

Target audience: Researchers with an interest in starting or continuing with Hi-C technique for non-model organisms in their research. Course streams include introductory, intermediate, and advanced levels.
Prerequisites - knowledge: Participants must have:

  • an understanding of fundamental genomics and epigenomics concepts
  • the ability to demonstrate basic laboratory technique, including safe laboratory practices

Participants should have:

  • an understanding of their local permit and safety requirements for processing and handling samples and reagents for HiC.

Structure and duration: Introductory stream - 2h40m video content
Challenging Sample stream - 3h20m video content
AssemblyLink stream - (TBD)
Discussion content - 3h15m video content
Expertise/skill level: Intermediate/Advanced. This course is intended for an audience familiar with labwork and research best practices.
Associated resources:
Arima Genomics Arima High Coverage HiC Kit User Guide for Animal Tissues (Document Part Number A160162 v01)
Dovetail AssemblyLink Kit User Guide (Version 1.0 May 30, 2024).

Access

URL to OER: https://scilifelab-training.github.io/BGE-HiC-course/
DOI: https://doi.org/10.5281/zenodo.14643653
Access cost: No
Events: None

Reuse

Licensing and reuse details:
The Arima HiC protocol used in this course is © 2019, Arima Genomics, Inc. All rights reserved.
The AssemblyLink protocol used in this course is © 2024, Cantata Bio, LLC. All rights reserved.
The video materials from this course are available for reuse under
Preferred citation: For citation of the entire course material, please use:

Maria Laura Aguilera Gil, Lorenzo Ballini, Laurie Bertrand, Simona Buonanno, Eunkyong Choi, Annunziata De Luisi, Giada Ferrari, Leonardo Girlanda, Carmela Gissi, Maria Gyftea, Brian Kilburn, Karine Labadie, Tuuli Lundback-Lärva, Graeme Oatley, Fernando Cruz Rodriguez, Irene Fabiola Roman Maldonado, Lily Shiue, Morten Skage, Pamela Veneziano Broccia, Ave Tooming-Klunderud, Olga Vinnere Pettersson (2025). Biodiversity Genomics Europe and SciLifeLab HiC Course. DOI:10.5281/zenodo.14643653.

Date of last revision: Aug 31, 2025
Status: Under development
Modification contact: training.hub@scilifelab.se
Version: v.1-partial