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Epigenetics

Methods to characterise genetic or transcriptomic differences other than the nucleotide composition, e.g. 3D conformation of chromatin or levels of methylation and other DNA/RNA base modifications.

Applications 4 Methods 9 Bioinformatics 5
DNA Methylation
Methods to determine the proportion of Cytosine methylation (5mC), the most common type of base modification in DNA.
ChIP-Sequencing
Chromatin immunoprecipitation sequencing (ChIP-seq) is used to analyze protein interactions with DNA across the genome.
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).
ATAC-Sequencing
The Assay for Transposase Accessible Chromatin (ATAC-seq) gives information on the open chromatin regions in a genome. We offer both bulk and single-cell ATAC-seq.
Enzymatic Methyl-seq (EM-seq)

NEBNext EM-Seq kit is an alternative to whole-genome bisulfite sequencing (WGBS). The enzymatic conversion of unmethylated cytosines in EM-seq is more gentle to DNA than WGBS and results in libraries with more even genome coverage and better coverage of CpG sites across the genome.

Arima HiC

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

ATAC-seq

A method to identify open chromatin regions, such as promotor areas, using a transposase.

Dovetail Omni-C

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

SPlinted Ligation Adapter Tagging (SPLAT) for Whole Genome Bisulphite Sequencing (WGBS)

SPLAT is an in-house developed WGBS library preparation method. This approach enables quick and efficient preparation of WGBS libraries from low-input DNA

SMARTer ThruPLEX DNA-seq

Library preparation for DNA, ideal for preparing libraries from small amounts of input material. Works well for shotgun libraries, ChIP DNA and FFPE samples, amongst others.

Nanopore DNA sequencing

Nanopore instruments can sequence very long continuous fragments of DNA. Sequencing native DNA allows detection of base modifications.

PacBio SMRT sequencing

PacBio SMRT sequencing generates reads tens of kilobases in length enabling high quality genome assembly, structural variant analysis, amplicon resequencing, full-length transcript isoform sequencing, full-length 16S rRNA sequencing and amplification free epigenetic characterization.

Illumina Infinium DNA Methylation EPIC Array

The EPIC BeadChip array allows for the interrogation over 850,000 methylation sites quantitatively across the genome at single-nucleotide resolution.

ATAC-seq analysis

Bioinformatic analysis pipeline for ATAC-seq data

Bisulfite-seq analysis

Runs with Bisulfite sequencing data. It pre-processes raw data from FastQ inputs, aligns the reads and performs extensive quality-control on the results, using either Bismark or bwa-meth/MethylDackel.

ChIP-seq analysis

Runs with ChIP sequencing data. Pre-processes raw data from FastQ inputs, aligns the reads and performs peak calling and extensive quality-control on the results.

PacBio secondary analysis

Analysis applications provided by NGI using PacBio’s open-source SMRT Analysis software suite.

Illumina QC analysis

Basic quality-control monitoring of Illumina FastQ sequence data.