Methods

Antibody-guided chromatin tagmentation (ACT-seq) enables the profiling of histone modifications and transcription factors.

Hi-ChIP profiles chromatin interactions coupled with a specific histone modification.

The assay for transposase-accessible chromatin with sequencing profiles open chromatin regions in the genome.

Illuminas microarrays enable the profiling of DNA methylation of a defined subset of CpGs at high sample throughput.

(tagmentation-based) Whole-Genome Bisulfite Sequencing profiles the methylation state of nearly all CpG dinucleotides in the human genome. We also established a protocol working with very low levels of input DNA.

EM-seq is an enzymatic alternative to WGBS.

snATAC-seq through 10x solution enables the profiling of open chromatin in single cells.

sRNA-seq through 10x solution enables the profiling of gene expression states in single cells.

Oxford nanopore sequencing enables the sequencing of long fragments of several thousand bases.

DiMeLo-seq profiles chromatin modification together with DNA methylation and stuctural variants across long genomic distances.

Pyjacker detect enhancer hijacking events in a cohort of at least 10 samples profiled with WGS and RNA-seq. It does not require matched normals and can detect enhancer hijacking events occurring in only a single sample. Briefly, it looks for outlier high and monoallelic expression of a gene in a sample which has a breakpoint close to the gene.

EpiCHAOS is a metric for calculating cell-to-cell heterogeneity in single-cell epigenomics data. EpiCHAOS can be applied to any single cell epigenomics dataset (e.g. scATAC-seq, scChIP-seq, scNMT-seq, scTAM-seq) in binarised matrix form.