A Streamlined Workflow to Perform ChIP from FFPE Samples

Abstract

Deciphering epigenetic alterations occurring during the onset and progression of diseases is critical to characterize human malignancies and help predict which therapeutic interventions will most likely improve clinical outcomes.  Because collections of malignant tissue as well as respective healthy controls exist in tissue banks, we developed a rapid and scalable extraction method to isolate chromatin from archived FFPE tissues suitable for ChIP.  Here, we demonstrate how the Adaptive Focused Acoustic® (AFA®) technology combined with truXTRAC® and truChIP® effectively recovers chromatin suitable for studying histone modifications and transcription factor binding interaction events.

Covaris DNA Shearing Guide for Illumina TruSight Tumor 170 NGS Assay

This document provides users with a complete set of protocols for
all current Covaris Adaptive Focused Acoustics® (AFA®) instruments
to use with the Illumina TruSight* Tumor 170 Kit. The following
protocols have been developed to deliver the best outcome and
compatibility for library preparation and subsequent sequencing
applications.

Optimized Covaris truXTRAC® FFPE RNA Protocol for Isolating RNA from Laser-Capture Microdissected (LCM) FFPE Tissue for Next Generation Sequencing

SUMMARY
It is well characterized that RNA extraction from FFPE tissues can be challenging, often producing low yields and/or poor-quality RNA which can adversely affect success of downstream applications such as Next-Generation Sequencing (NGS). In this application note we describe an optimized workflow using Covaris truXTRAC FFPE RNA kits with deparaffinized, stained LCM-FFPE tissues of cancerassociated stroma (CAS) and matched normal stroma derived from canine mammary tumors. Using this adapted truXTRAC workflow, compared to the classical protease-based RNA isolation methods, total RNA yields were increased by 8- to 12-fold and RT-qPCR Cq values were 2.3-fold lower on average, signifying better performance. Finally, this improved quantity and quality of RNA performs favorably well in NGS workflows, overcoming the challenges of using low input RNA in RNA sequencing.

Optimized protocol for robust chromatin shearing and immunoprecipitation of human pancreatic islets using the Covaris® Focused-ultrasonicator

In this application note, Escalada et al. processed human islet cells for ChIP-Seq and ChIP-qPCR using the S220 Focused-ultrasonicator. The authors developed a protocol using the focused acoustics shearing platform to compare its performance to other traditional methods including: probe and water bath sonication. Pre-sequencing fragment size analysis data is presented as well as ChIP-qPCR and ChIP-Seq results.