SX-8G IP-Star® Compact Automated System

This application note demonstrates the automation of ChIP using the SX-8G IP-Star Automated System, allowing the entire ChIP procedure to be performed in a single day. Chromatin Immunoprecipitation (ChIP) is a type of immunoprecipitation experimental technique used to investigate the interaction between proteins and DNA in the cell. It aims to determine whether specific proteins are associated with specific genomic regions, such as transcription factors on promoters or other DNA binding sites, and possibly defining cistromes. ChIP also aims to determine the specific location in the genome that various histone modifications are associated with, indicating the target of the histone modifiers.

Chromatin immunoprecipitation (ChIP) is the most widely used method to study protein-DNA interactions. ChIP followed by HTS (ChIP-seq) enables the extension of the target directed analysis of ChIP results to a genome wide analysis. In view of the enormous potential and growing interest of this new development and to increase the quality standards of their antibodies, Diagenode has added this new technique to their QC procedure. This poster presents 19 ChIP-seq grade antibodies analyzed using the SX-8G IP-Star® Compact.

ChIP experiments require long and multi-step protocols, and the risk of introducing inconsistency is very high. The goal of this experiment was to confirm the findings from ChIP sequencing by using an automated ChIP technology in order to reduce all inconsistency introduced by the pipetting variations and human variability. This application note presents high sensitivity automated ChIP experiments to study transcriptional regulation and siRNA technology. The study used the Bioruptor UCD-300-TO with associated reagents for chromatin preparation and the SX-8G IP-Star® Compact Automated System with associated reagents for ChIP and an ETO antibody for the immunoprecipitation step.

The pairing of traditional expression assays with high-throughput sequencing (RNA-seq) has allowed the generation of genome-wide gene expression data with unparalleled specificity, throughput, and sensitivity delivering an unbiased representation of the transcriptome. However, full genome transcriptional gene characterization has been partially limited by the complexity and increased time-requirements of available RNA-seq library construction protocols. Here we report the successful application of the Diagenode IP-Star® Compact System for the easy, rapid, and reproducible RNA-seq library construction of five Mus musculus (mouse) samples. Use of the IP-Star® Compact System significantly reduces the hands-on time required and results in high-quality, highly reproducible RNA-seq libraries tailored for Illumina high-throughput next-generation sequencing. The IP-Star® Compact System is an efficient and reliable tool for the construction of next-generation RNA-seq libraries, especially for transcriptome-based annotation of larger genomes or genomes with many alternative gene isoforms.

Watch this video to learn how Diagenode, the leader in the field of epigenetics, provides full solutions for your chromatin immunoprecipitation and DNA methylation research with its wide range of automation instruments.