NGI during Covid-19 outbreak

NGI is still up and running during the Covid-19 pandemic, but we are experiencing some limitations in terms of personnel and key reagents. Each NGI node is following its respective host university recommendations and will continue operation until further notice.

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HiC

A method to characterise genome-wide chromatin contacts. Can be used to investigate the 3D genome organisation in the nucleus, eg. to study topologically-associated functional domains (TADs).

The method involves preparation of a sequencing library from snap frozen tissues or cells by the means of restriction enzyme digestion, followed by proximity ligation to capturing genome organisation within a ligated molecule. Ligated library molecules are then sequenced as paired-end reads to reveal which of the genome were physically proximal in the nuclei at the time of sampling. The method can be used to investigate the Topologically Associated Domain (TAD) architecture of cells or tissues, as well as error-correction of de novo genome assemblies.

We are offering HiC library creation by means of kits from Arima Genomics and Dovetail Genomics. Both kits have been shown to produce high-quality libraries from a range of different samples, e.g. plant material as well as animal cells and tissues.

Arima HiC

Production of high-quality proximity ligation libraries, using two restriction enzymes.

Dovetail Omni-C

A proximity-ligation protocol using a sequence-independent endonuclease, generating data for TAD identification and scaffolding.