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 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.

Preparation of whole body Caenorhabditis elegans extracts for chromatin immunoprecipitation using the Covaris® S220 Focused-ultrasonicator

Focus: Ruben et. al. from Boston University School of Medicine developed a ChIP-Seq sample preparation protocol for whole body C. elegans extracts. The authors of this application note provide a step-by-step sample preparation workflow and highlight the key advantages of using the Covaris S220 Focused-ultrasonicator.

Covaris DNA shearing guide for the Agilent SureSelect Target Enrichment System©

This document provides users with a complete set of protocols that encompass all Covaris Adaptive Focused Acoustics™
(AFA) instruments for DNA shearing to 150 to 200 bp with 50 to 55 µl of sample volume, to be readily compatible with the Agilent SureSelect Target Enrichment System (XT or XT2). The goal is to provide the most precise, pre-validated protocols to ensure the best outcome and compatibility for library preparation and subsequent sequencing applications.