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.
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.
epigenetics illumina CpG WGBS EM-seq library preparation methylationProduction of high-quality proximity ligation libraries, using two restriction enzymes.
illumina de novo chromatin scaffolding library preparation epigenetics TADsA method to identify open chromatin regions, such as promotor areas, using a transposase.
ATAC open chromatin epigenetics illumina ATACseq ATAC-seqA proximity-ligation protocol using a sequence-independent endonuclease, generating data for TAD identification and scaffolding.
chromatin scaffolding library preparation epigenetics TADs illumina de novoSPLAT is an in-house developed WGBS library preparation method. This approach enables quick and efficient preparation of WGBS libraries from low-input DNA
WGBS Bisulphite single-stranded DNA ssDNA library preparation methylation epigenetics illumina CpGLibrary 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.
genome illumina WGS dna library preparationNanopore instruments can sequence very long continuous fragments of DNA. Sequencing native DNA allows detection of base modifications.
assembly long-read nanoporePacBio 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.
hifi clr de novo iso seq sv smrt assembly pacbio methylation amplicon sequelThe EPIC BeadChip array allows for the interrogation over 850,000 methylation sites quantitatively across the genome at single-nucleotide resolution.
methylation epigenetics illumina dna array infinium CpGBioinformatic analysis pipeline for ATAC-seq data
ATACseq ATAC-seq chromatin open chromatinRuns 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.
methylseq Methyl-Seq BS BisulfiteRuns 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.
ChIP-Seq chipseqBasic quality-control monitoring of Illumina FastQ sequence data.
QC fastqc fastq screen checkqc