Hi-C Knowledge Exchange
HiC chemistry and validation
The companies producing and validating the protocols and chemistries used in the course presented about their kits. To view these presentations, including an overview of the chemistry as well as validation information, please see the videos linked below.
AssemblyLink - Cantata Bio
|
Miles Collier, Cantata Bio, presents on AssemblyLink |
The AssemblyLink protocol used in this course can be found here.
Arima Genomics
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Brian Kilburn, Arima Genomics, presents on the Arima HiC protocol. |
The Arima HiC protocol used in this course can be found here.
Protocol adaptations and tips
A representative from each institution presented specific adaptations and information on best practices for their sample processing, including a bioinformaticians view of HiC from Fernando Cruz Rodriguez.
| Practice | Presented by | Runtime |
|---|---|---|
| Considerations for tissue grinding | Karine Labadie, Genoscope | 17min |
| Nuclei isolation from plant samples | Giada Ferrari, University of Oslo | 10min |
| Ultra low input samples | Irene Fabiola Roman Maldonado, The Sanger Institute | 10min |
| A bioinformatic view of HiC QC | Fernando Cruz, CNAG | 51min |
Challenging Samples Discussion
Prior to the course, the challenging samples were sent to the participating institutions for processing. Each institution presented their own handling of samples, including nuclei isolation, kits, what organisms they had success with, as well as sample outcomes–including with the AssemblyLink kit.
| Organisms | Presented by | Runtime |
|---|---|---|
| Plants and Algae | Karine Labadie, Genoscope | 16min |
| Plants and Lichens | Irene Fabiola Roman Maldonado, The Sanger Institute | 16min |
| Coral and Sponge | Brian Kilburn, Arima | 8.5min |
| Jellyfish and Coral | Karine Labadie, Genoscope | - |
| Monogyna spp. | Morten Skage, University of Oslo | 5min |
| Fish Blood - AssemblyLink | Morten Skage, University of Oslo | coming soon |
| Worms and Algae - AssemblyLink | Lily Shiue, Cantata Bio | coming soon |
Morten Skage, University of Oslo, presents considerations for how to define and approach challenging samples. Runtime: 14 min.
Full HiC Protocol Knowledge Playlist
Citation
The Arima HiC protocol used in this course is © 2019, Arima Genomics. The AssemblyLink protocol used in this course is © 2024, Cantata Bio, LLC. All rights reserved.
The video materials from this course stream are available for reuse under 
Individual lectures should be cited with credit given to the presenting researcher. If citing this page in its entirety, please use:
Fernando Cruz, Giada Ferrari, Brian Kilburn, Karine Labadie, Irene Fabiola Roman Maldonado, Lily Shiue, Morten Skage, Ave Tooming-Klunderud, Olga Vinnere Pettersson (2025). Biodiversity Genomics Europe and SciLifeLab Knowledge Exchange Collection. Retrieved from https://scilifelab-training.github.io/BGE-HiC-Course/protocols.html