Application Note: Pairing Covaris truXTRAC(TM) FFPE RNA pre-analytical extraction with the NanoString Technologies nCounter Analysis System for streamlined analytical assays.

Application Note: Pairing Covaris truXTRACTM FFPE RNA pre-analytical extraction with the NanoString Technologies nCounter Analysis System for streamlined analytical assays.

Chromosome Conformation Capture Using Biotinylated Oligos – Capture-C

Chromosome Conformation Capture Using Biotinylated Oligos – Capture-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
  • Capture-C7 and its refinement NG Capture-C8 provides a powerful tool to study long-range interactions with high sensitivity allowing for relatively low input amounts

Advantages of Adaptive Focused Acoustics® (AFA®)

  • Random shearing guarantees an unbiased fragmentation of ligation products which reduces PCR biases and cost per sample
  • 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

Shallow Whole Genome Sequencing Workflow – sWGS

Shallow Whole Genome Sequencing Workflow – sWGS

Scientific Relevance

  • Tumor-sequencing studies have demonstrated that most cancers are driven by either single-nucleotide variants (SNV) or structural variants (SV)
  • Shallow Whole Genome Sequencing (sWGS), also known as Low Coverage (LC) WGS, allows researchers to determine SV with 0.1 to 0.2X low sequencing coverage
  • Low-cost sWGS is emerging as a promising clinical sequencing strategy for SV-driven tumors1
  • sWGS can be used for clinically relevant structural variants such as oncogenic amplification, tumor-suppressor deletion, and genomic instability
  • sWGS can be applied to DNA originating from Formalin-Fixed Paraffin-Embedded tissue (FFPE), blood, or cfDNA

Advantages of Adaptive Focused Acoustics® (AFA®)

  • Highly reproducible results
  • Unbiased fragmentation regardless of GC content
  • Compatible with all DNA inputs, quality, and origin, including FFPE samples
  • Automation-friendly options (LE220R-plus paired with oneTUBE-10™ consumables)

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