Challenging Samples
The group who worked with the challenging samples consisted of Giada Ferrari (University of Oslo, NO), Pamela Veneziano Broccia (CNAG, ES), Tuuli Lundbäck-Larva (SciLifeLab, SE), and Brian Kilburn (Arima, US). All group participants have previous experience of HiC, and contributed specialized knowledge of challenging sample preparation.
- The challenging samples content is currently in post-production and access is limited to participants
- If you require access, please contact the course administrators
Sample preparation
Eight challenging sample types were processed for Hi-C. Watch the following videos for a walkthrough of each sample up to the crosslinking step.
Lichens
Two lichen samples were processed by grinding in liquid nitrogen in a mortar and pestle. Runtime: 30 minutes.
Flustra
The Flustra sample was ground using liquid nitrogen as for the Lichen samples. Runtime: 2.5 minutes.
Sponge
A sponge was processed using the “squeeze method”; a gentle extraction of nuclei from the sponge skeleton. Runtime: 30 minutes.
Algae (slime)
Processing of an algae that produces an extracellular matrix. Runtime: 5 minutes.
Mosquitos
Sample processing of mosquitos. Two different sample preparations were performed. Runtime: 15 minutes.
Worm
Discussion of sample processing - one individual crosslinked in its entirety and dissolved easily without further disruption. Runtime: 2 minutes.
Crosslinking
The eight sample types were batch processed from the crosslinking stage onwards. Includes discussion on handling insects, low input samples, recommended equipment, and sticky pellets. Runtime: 26 minutes.
Estimating Input
The estimating input protocol was performed on the two lichen samples. Runtime: 22 minutes.
HiC Reactions
Follow the challenging samples group as they perform the enzymatic reactions on the challenging samples. Kai from Arima joins for day 3 of the protocol! Runtime: 60 minutes.
QC1
The last step for the challenging reactions is to follow the QC1 protocol. Runtime: 15 minutes.