Simplifying ChIP from Primary Cells and Clinical Samples for High-throughput Epigenetic Applications

Simplifying ChIP from Primary Cells and Clinical Samples for High-throughput Epigenetic Applications

Abstract: Large-scale analysis of histone marks and transcription factor interactions requires high-quality chromatin, use of validated Chromatin Immunoprecipitation (ChIP)-grade antibodies, and optimized reagents to produce meaningful and reproducible results. In this application note, we demonstrate:

i. Isolation of nuclei using Covaris Adaptive Focused Acoustics® (AFA®) technology followed by purification using a sucrose ultracentrifugation step standardizes ChIP workflows and enables scientists to process-hard-to-lyse samples and reduce input requirements, which is frequently encountered when working with clinical samples.
ii. Pairing Covaris truChIP Kits with Chromatrap bead-free immunoprecipitation (IP) technology provides a simple, sensitive, and scalable workflow for downstream applications, such as ChIP-qPCR and ChIP-seq.

Cell Lysis and High Molecular Weight DNA Extraction from Eukaryotic and Prokaryotic Cells Powered by AFA-Engergetics

This application note describes a novel automatable approach to cell lysis and extraction of high molecular weight (HMW) DNA (>30,000 base pairs) from microbial samples, which can be readily sequenced with long-read sequencing technologies such as PacBio or Oxford Nanopore. Lysing the cells and subsequent extraction of HMW DNA from microbial samples is achieved on a Covaris LE220-plus Focused-ultrasonicator using a non-contact method mediated by AFA. Rapid lysis is achieved in less than 2 minutes for 96 individual bacteria samples and 10 to 60 minutes for 96 individual yeast samples when using a PCR-compatible 96 oneTUBE-10 AFA Plate. Both electropherograms and Qubit measurements reveal that high molecular weight DNA can be efficiently extracted using AFA-mediated cell lysis.

High-Throughput, Low Volume gDNA Extraction from Whole Blood Enabled by Covaris Adaptive Focused Acoustics® (AFA®) and oneTUBE-10

Extraction of genomic DNA (gDNA) from whole blood is the first step in multiple translational research and molecular diagnostics applications, such as next-generation sequencing (NGS), multiplex PCR, qPCR, and droplet digital PCR (ddPCR). For example, DNA from whole blood is frequently used as a matched-control for solid tumor somatic mutation profiling and for the detection of clinically-relevant variants in hematological malignancies. An increasing number of clinical studies demonstrate the value of detecting disease-specific biomarkers from blood for diagnosis, treatment monitoring, and cohort study recruitment.

Covaris Shearing Guide for 500 Base Pairs using the 96 oneTUBE-10 AFA Plate

Covaris Shearing Guide for 500 Base Pairs using the 96 oneTUBE-10 AFA Plate