# Protocol to isolate nuclei from Chlamydomonas reinhardtii for ATAC sequencing

## TL;DR

This paper provides a fast and efficient protocol to isolate nuclei from the green alga Chlamydomonas reinhardtii for ATAC-seq, suitable for both cell-walled and cell wall-deficient strains.

## Contribution

A novel, optimized, tag-free protocol for isolating high-quality nuclei from Chlamydomonas reinhardtii for ATAC-seq.

## Key findings

- The protocol enables efficient nuclei isolation from both cell-walled and cell wall-deficient strains of Chlamydomonas reinhardtii.
- The method is optimized to reduce the time required for nuclei isolation and quantification.
- The isolated nuclei are of sufficient quality for ATAC-seq experiments.

## Abstract

The isolation of sufficient amounts of intact nuclei is essential to obtain high-resolution maps of chromatin accessibility via assay for transposase-accessible chromatin using sequencing (ATAC-seq). Here, we present a protocol for tag-free isolation of nuclei from both cell walled and cell wall-deficient strains of the green model alga Chlamydomonas reinhardtii at a suitable quality for ATAC-seq. We describe steps for nuclei isolation, quantification, and downstream ATAC-seq. This protocol is optimized to shorten the time of isolation and quantification of nuclei.

•Optimized isolation of nuclei from the green model alga Chlamydomonas reinhardtii•Tag-free isolation from both cell-walled and cell wall-deficient algae strains•Key steps for an effective and fast isolation and quantification procedure of nuclei•Extracts at a quality suitable for ATAC-sequencing

Optimized isolation of nuclei from the green model alga Chlamydomonas reinhardtii

Tag-free isolation from both cell-walled and cell wall-deficient algae strains

Key steps for an effective and fast isolation and quantification procedure of nuclei

Extracts at a quality suitable for ATAC-sequencing

Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.

The isolation of sufficient amounts of intact nuclei is essential to obtain high-resolution maps of chromatin accessibility via assay for transposase-accessible chromatin using sequencing (ATAC-seq). Here, we present a protocol for tag-free isolation of nuclei from both cell-walled and cell wall-deficient strains of the green model alga Chlamydomonas reinhardtii at a suitable quality for ATAC-seq. We describe steps for nuclei isolation, quantification, and downstream ATAC-seq. This protocol is optimized to shorten the time of isolation and quantification of nuclei.