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.
library preparation methylation epigenetics illumina CpG WGBS EM-seqProduction 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.
Omni-ATAC TN5 ATAC open chromatin epigenetics illumina ATACseq ATAC-seqA proximity-ligation protocol using a sequence-independent endonuclease, generating data for TAD identification and scaffolding.
scaffolding library preparation epigenetics TADs illumina de novo chromatinSPLAT is an in-house developed WGBS library preparation method. This approach enables quick and efficient preparation of WGBS libraries from low-input DNA
Bisulphite single-stranded DNA ssDNA library preparation methylation epigenetics illumina CpG WGBSLibrary 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.
methylation amplicon sequel hifi clr de novo iso seq sv revio smrt assembly pacbioThe EPIC BeadChip array allows for the interrogation over 935,000 methylation sites quantitatively across the genome at single-nucleotide resolution.
CpG methylation epigenetics illumina dna array infiniumBioinformatic analysis pipeline for ATAC-seq data
ATACseq ATAC-seq chromatin open chromatinRuns with methylation 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