Table 4 Genetic and epigenetic measurement tools
Name | Type | Purpose | Example |
|---|---|---|---|
Oxford Nanopore Technologies [111] | Sequencing Platform | Long-read genome and epigenetic sequencing | Used for direct detection of methylation patterns from DNA molecules without bisulfite conversion |
EM-seq [112] | Next-Generation Sequencing | Enzyme-based DNA methylation sequencing | Indirect detection of DNA methylation patterns through enzymatic treatment |
DM-Seq [113] | Next-Generation Sequencing | Direct detection of methylation sequencing on DNA molecules | Offers an all-enzymatic, non-destructive, faithful, and direct method for the reading of 5-methylcytosine |
PacBio Sequel II [114] | Sequencing Platform | Single Molecule Real-Time (SMRT) sequencing | Provides long reads and high accuracy for genome sequencing, useful for structural variant and complex region analysis |
10 × Genomics Chromium [115] | Single-Cell Analysis Platform | Single-cell transcriptome and genome sequencing | Enables transcriptomic analysis of thousands of single cells to reveal cellular heterogeneity |
Illumina NovaSeq [9] | Sequencing Platform | High-throughput genome and transcriptome sequencing | Used for large-scale whole-genome sequencing, exome sequencing, and RNA-seq, suitable for GWAS and transcriptomic studies |
Bisulfite Sequencing [116] | DNA Methylation Sequencing Technique | DNA methylation analysis | Involves treating DNA samples with sodium bisulfite followed by sequencing to identify methylated cytosines |
ATAC-seq [117] | Chromatin Accessibility Sequencing Technique | Open chromatin region analysis | Utilizes Tn5 transposase to tag open chromatin regions followed by sequencing to study chromatin accessibility |
ChIP-seq [118] | Chromatin Immunoprecipitation Sequencing Technique | Protein-DNA interaction analysis | Identifies the binding sites of specific proteins (e.g., transcription factors or histone modifications) on DNA |
Hi-C [119] | Chromosome Conformation Capture Technique | 3D genome structure analysis | Studies the spatial organization of chromatin within the nucleus, revealing interactions between distant regulatory elements |
Single-cell bisulfite sequencing [120] [e.g. smart RRBS [121], sci-Met [122]] | Single-Cell Sequencing Technique | Single-cell analysis | Analyzes patterns at the single-cell level, providing information on epigenetic heterogeneity between cells |
Drop-seq [123] | Single-Cell Analysis Platform | Single-cell transcriptome analysis | Uses microfluidics to capture and sequence RNA from individual cells, enabling gene expression analysis at the single-cell level |