Diagenode Tissue Nuclei Extraction for ATAC-seq

Diagenode’s Tissue Nuclei Extraction for ATAC-seq module has been developed and validated for efficient nuclei extraction from tissue samples prior to ATAC-seq experiment. The protocol has been validated on many different tissues (lung, liver, brain, kidney, muscles) and different species (pork, chicken).

For a complete ATAC-seq for tissue workflow we highly recommend to use the ATAC-seq package for tissue. The ATAC-seq package includes all reagents needed for nuclei extraction from tissues, library preparation and multiplexing. For more details please go to the page: ATAC-seq package for tissue.

Features:

• Starting amount: 25 mg – 100 mg per rxn
• Validated on many mammalian tissues
• Included in a complete ATAC-seq workflow: ATAC-seq package for tissue

ATAC-seq, Assay for Transposase-Accessible Chromatin, followed by next generation sequencing, is a key technology to easily identify the open regions of the chromatin. The protocol consists of 3 steps: nuclei preparation, tagmentation and library amplification. First, the tissue undergo the lysis, ending with the crude nuclei. Then, the nuclei are incubated with a tagmentase (Tn5 transposase), which  cuts the genomic regions associated with open chromatin and inserts the sequencing adaptors. Finally, the generated libraries are amplified and can be used for sequencing. High-throughput sequencing will then detect peaks, in open regions of the chromatin only, giving a map of the chromatin status in the whole genome of the sample.

 Example of results

GENE-SWitCH aims to deliver new underpinning knowledge on the functional genomes of two main monogastric farm species (pig and chicken) and to enable immediate translation to the pig and poultry sectors. It is a multi-actor project that will produce new genome information to enable the characterization of genetic and epigenetic determinants of complex traits in these two species. Diagenode, as a principal participant to the project and leading the WP1, developed a new protocol to improve the preparation of ATAC-seq libraries from a variety of snap-frozen tissues. The ATAC-seq protocol combines efficient nuclei extraction procedure validated on 7 different kinds of tissues from 3 developmental stages of the two species and a robust Tagmentation protocol based on Diagenode Tn5 enzyme. The developed ATAC-seq protocol was successfully used to produce 168 ATAC-seq libraries for WP1 and 320 for WP5.

Table 1. List of validated tissues with Diagenode’s ATAC-seq package for tissue (Cat. No. C01080005/6). The samples were used as part of GENE-SWitCH consortium.

A.

B.

Figure 2. ATAC-seq library profiles generated using the ATAC-seq package for tissue (Cat. No. C01080005/6) from pork’s liver (A) and brain (B). The samples were used as part of GENE-SWitCH consortium.