HiC Chromatin Immunoprecipitation – HiCHIP

HiC Chromatin Immunoprecipitation – HiCHIP

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
  • HiChIP provides a powerful tool to uncover proteins involved in 3D chromatin organization especially suited for low input samples

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 non-specific interactions
  • Reproducible shearing allows reliable comparison of samples from different origins such as cancer subtypes or different stages of progressive diseases
  • Reproducibility and efficiency of shearing allows for small input amounts

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