The complexity of cellular behaviors exceed beyond the sequence of the genome. DNA methylation states, histone modifications, chromatin accessibility and the 3-dimensional spacial arrangements of chromatin are important factors working in concert to define global gene expression pattern of every single cell. Understanding these critical aspects, in bulk and in single-cell level, will grant us new perspectives of the cell.

To interrogate the epigenome and transcriptome of various samples, we follow a set of standardized protocols.

Protocols

  • Chromatin Immunoprecipitation (ChIP) – We use ChIP to obtain the proteins that bind to the chromatin. Histone, the packaging protein of genomes, can be post translationally modified which have substantial effects on gene activities. ChIP against different histone modifications can reveals the activity of genes.
    • Native ChIP
    • μChIP
  • ChIP-seq – We couple ChIP with next-generation sequencing to profile the protein-genome interaction.
    • ChIP-seq
  • Whole Genome Bisulphite Sequencing – Bisulphite treatment discriminate cytosine from 5-methylcytosine. By coupling bisulphite treatment with whole genome sequencing, we can assess the DNA methylation states of cells at single-base resolution.
  • RNA-seq – We profile the transcriptome by performing next-generation sequencing on RNA
    • RNA-seq
    • Smart-Seq2
  • Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) – Some regulatory elements act on accessible region on the chromatin. We locate the accessible chromatin region by the use of transposase in ATAC-seq.
    • ATAC-seq
    • OMNI-ATAC-seq
  • High-throughput Chromatin Conformation Capture (Hi-C) – 3-dimensional spacial arragnement of the chromatin allow long-range gene interaction. By using Hi-C technology, we can profile high-order genome organization.
    • sisHi-C

Please contact us for more information