High-resolution Chromosome Conformation Capture: Hi-C

High-resolution Chromosome Conformation Capture: Hi-C

Scientific Relevance

  • Three-dimensional chromatin organization regulates gene expression
  • Aberrant chromatin looping causes altered gene regulation in malignancies including solid tumors as well as hematologic neoplasms
  • Characterization of 3D-chromosomal conformations allows classification of cancer subtypes
  • Cancer progression can be alleviated by inhibiting certain chromatin loop formations
  • Hi-C provides a powerful tool to better characterize 3D chromatin organization and helps to uncover the impact of cancer risk-associated SNPs

Advantages of Adaptive Focused Acoustics® (AFA®)

  • Random shearing guarantees an unbiased fragmentation of ligation products
  • The tight size distribution ensures comprehensive representation of all ligation junctions in the sequencing library
  • Reproducible shearing allows reliable comparison of samples from different origins such as cancer subtypes or different stages of progressive diseases

Chromatin Interaction Analysis by Paired-End Tag Sequencing – ChIA-PET

Chromatin Interaction Analysis by Paired-End Tag Sequencing – ChIA-PET

Scientific Relevance

  • Three-dimensional chromatin organization regulates gene expression
  • Aberrant chromatin looping causes altered gene regulation in malignancies including solid tumors as well as hematologic neoplasms
  • Characterization of 3D-chromosomal conformations allows classification of cancer subtypes
  • Cancer progression can be alleviated by inhibiting certain chromatin loop formations
  • ChIA-PET provides a powerful tool to uncover proteins involved in 3D chromatin organization

Advantages of Adaptive Focused Acoustics® (AFA®)

  • Good epitope preservation allows for comprehensive enrichment of sequences bound by the protein of interest
  • The tight size distribution reduces the pull-down of nonspecific interactions
  • Reproducible shearing allows reliable comparison of samples from different origins such as cancer subtypes or different stages of progressive diseases

Nuclei EXtraction by SONication – NEXSON

Nuclei EXtraction by SONication – NEXSON

Scientific Relevance

  • ChIP-Seq is a powerful tool to map DNA binding proteins as well as histone modifications across the genome
  • To allow the comparison of different studies and different input materials standardization of the sample preparation steps are required, which has been challenging
  • NEXSON provides a simple but highly reproducible technique for efficient nuclei isolation, ensuring the generation of comparable chromatin maps from different sample types

Advantages of Adaptive Focused Acoustics® (AFA®)

  • The high efficiency of nuclei isolation allows the scale down of input material to 10,000 cells/histone ChIP and 100,000 cells/transcription factor ChIP
  • Increased robustness permits comparison across different tissues, cell types, disease stages, and laboratories
  • The highly reproducible and efficient isolation of nuclei allows for novel high throughput derivates of ChIP technology

Nucleic Acid Extraction from Laser-Capture Microdissected (LCM) FFPE Tissues

Nucleic Acid Extraction from Laser-Capture Microdissected (LCM) FFPE Tissues

Scientific Relevance

  • Formalin-fixed, paraffin-embedded (FFPE) tissue is a widely used method for long-term clinical sample storage, but it comes with significant drawbacks due to the harsh nature of this method
  • Researchers are increasingly realizing the importance of investigating subpopulations of cells within homogeneous tissue and the cross-talk between these cells, especially for tumor cells and their surrounding stroma
  • Laser-Capture Microdissection (LCM) can be used on FFPE tissues and enables researchers to target and collect subsets of cells for DNA and RNA analysis by examining the tissue structure through microscopy

Advantages of Adaptive Focused Acoustics® (AFA®)

  • Efficient extraction of high-quality nucleic acids from FFPE tissues that can be used in PCR, qPCR, and NGS
  • Reduced QNS rates with even the smallest inputs
  • Longer RNA fragments with high DV200 scores, enabling detection of rare fusion events
  • Simultaneous RNA and DNA extraction from the
    same FFPE tissue