In addition to single-cell RNA sequencing (scRNA-seq), single-cell assays for transposase-accessible chromatin sequencing (scATAC-seq) provide epigenomic analyses that are increasingly used in plant tissue studies. As an industry-leading plant technology company, Lifeasible offers an improved scATAC-seq technology platform to identify and characterize highly accessible plant chromatin regions.

Introduction to Plant scATAC-seq

Plants must precisely regulate their transcription in response to their environment and proper development, growth, and homeostasis in vivo. Transcription is associated with relatively open chromatin regions where cis-regulatory elements such as enhancers and promoters can recruit transcription factors and RNA polymerase II to transcribe DNA. An improved method for identifying accessible regions where chromatin and transcription factors bind is the single-cell assay for transposase-accessible chromatin sequencing (scATAC-seq) technology. This method uses an extremely active Tn5 transposase to integrate pre-loaded sequencing junctions into open chromatin regions. Currently, transposase-accessible chromatin sequencing (ATAC-seq) coupled with microfluidic isolation and cell barcoding assays have become a powerful method for studying chromatin accessibility in individual plant cells.

Fig.1. ATAC-seq profiling using nuclei isolated by INTACT or sucrose sedimentation. (Bajic M, et al., 2018)

What We Offer

Lifeasible is a pioneer in plant biotechnology, offering a comprehensive service for plant single-cell transposase accessible chromatin sequencing (scATAC-seq) that allows studying cell-specific chromatin accessibility in plants at single-cell resolution. With our state-of-the-art equipment and molecular biology expertise, we can use ATAC-seq in combination with high-throughput sequencing to map plant-accessible chromatin signatures. Our services cover every step of the scATAC-seq workflow, ensuring accurate and reliable results.

(1) Sample Preparation and Nucleus Isolation

The isolation of high-quality nuclei is essential for obtaining reliable and informative data. Lifeasible provides expert assistance in sample preparation and nuclei isolation for scATAC-seq. We use optimized protocols to isolate total nuclei from Arabidopsis tissues or to isolate nuclei from specific cell types. By removing interfering organelle DNA, we can improve the efficiency of Tn5 translocation, resulting in more accurate identification of chromatin accessible regions.

(2) Library Construction and scATAC-seq

Our advanced laboratory facilities allow us to perform efficient and streamlined library construction for scATAC-seq. We utilize overactive Tn5 transposase to cleave DNA while inserting sequencing junctions into open chromatin regions of isolated nuclei, critical for capturing the chromatin accessibility landscape at single-cell resolution. With our state-of-the-art sequencing platform, we generate high-quality sequencing data that allows for comprehensive analysis of plant single-cell epigenomes.

(3) Computational Analysis and Data Interpretation

Lifeasible specializes in the computational analysis and data interpretation of scATAC-seq experiments. Our bioinformatics experts use sophisticated algorithms and pipelines to process and analyze the acquired data. We reveal the intricate linkages between chromatin accessibility and gene expression by combining scATAC-seq data with other histological datasets (scRNA-seq).

Our Methods for Purifying Plant Nuclei for scATAC-seq

Applying scATAC-seq in plant tissues has been challenging because it is difficult to isolate nuclei that are sufficiently free of interfering organelle DNA. We offer two different methods to purify plant nuclei for scATAC-seq:

• We use an extraction buffer containing a non-ionic detergent to lyse the organelles, followed by sucrose precipitation to purify the nuclei further. This method of nucleus isolation can be performed in any laboratory on most plant tissues.
• Nuclei isolation in specific cell types labeled methods to isolate nuclei from tissues or specific cell types. A key advantage of this method is not only that the isolated nuclei have less organelle DNA contamination but also that this method can be used to selectively isolate nuclei from specific cell types.

Our experimental procedures, particularly scATAC-seq using sucrose precipitation of purified nuclei, can be easily adapted for chromatin analysis of any plant species. Lifeasible's scATAC-seq services enable researchers to explore the complex regulatory mechanisms behind plant gene expression and have been widely used to explore gene regulation, elucidate regulatory networks, and even at a finer scale to classify plant cell types. If you are interested in our services or have some questions, please feel free to contact us or make an online inquiry.

Reference

1. Bajic M, Maher KA, Deal RB. Identification of Open Chromatin Regions in Plant Genomes Using ATAC-Seq. Methods Mol Biol. 2018;1675:183-201.

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Related Services

• Plant Single-cell RNA Sequencing (scRNA-seq) Analysis
• Plant Single-cell RNA Sequencing (scRNA-seq)
• Plant Single-cell Assay for Transposase-Accessible Chromatin Sequencing (scATAC-seq) Analysis
• Single-cell Solutions for Plant Research