Single-cell assay for transposase-accessible chromatin sequencing (scATAC-seq) characterizes the plant chromatin accessibility landscape at the single-cell level, thereby revealing intercellular variability in gene regulation. However, the high dimensionality and sparseness of scATAC-seq data often complicate the analysis. Lifeasible uses bioinformatics tools to help clients analyze and interpret plant scATAC-seq data. Our unique skills in data analysis will exceed our client's expectations of personalized data analysis and provide the most comprehensive data analysis results.

Introduction to Plant scATAC-seq Analysis

In eukaryotes, gene expression is highly correlated with open chromatin, which can be mapped by high-throughput ATAC-seq analysis of transposase-accessible chromatin. Recently, ATAC-seq has been applied to the complex organization of single cells in a variety of multicellular eukaryotic species, including two plants, namely Arabidopsis thaliana, and maize. Consistent with the important role of chromatin state on gene expression, these studies identified different chromatin patterns in different tissues and cell types and revealed key regulatory sequences that, in turn may be associated with transcription factors (TFs). However, discrete, sparse, and noisy scATAC-seq data pose a significant challenge for data analysis. Recently, several new computational tools have been developed for single-cell regulatoryome analysis, including chromVAR, SCRAT, and BROCKMAN.

Fig.1. Single-cell ATAC-seq and cluster annotation of rice root tips. (Feng D, et al., 2022)

What We Offer

Lifeasible offers a comprehensive data analysis process for plant scRNA-seq. Our team of experienced bioinformaticians and plant biologists is dedicated to providing our customers with the most accurate and reliable data analysis solutions to enable them to gain a deeper understanding of the regulatory dynamics of the plant genome.

(1) Data Pre-processing and Quality Control

We provide state-of-the-art tools and algorithms to pre-process scATAC-seq data, including read alignment, duplicate removal, and quality assessment. By utilizing advanced filtering techniques, we ensure high-quality data and reduce noise and artifacts that can affect downstream analysis.

(2) Cell Type Identification and Clustering Analysis

We utilize sophisticated computational methods such as descending and clustering algorithms to identify cell types based on chromatin accessibility profiles. By accurately classifying cells into subgroups, it helps you gain information on cell type-specific regulatory programs and their role in plant development and environmental responses.

(3) Differential Accessibility Analysis

Lifeasible uses state-of-the-art statistical methods and tools to identify Differential Accessible Regions (DARs) and genes. By comparing scATAC-seq profiles between different conditions or cell types, it helps you unravel the regulatory mechanisms behind developmental processes, stress responses, and other biological issues.

(4) Integrated Analysis with Other Allometric Data

Lifeasible provides an advanced bioinformatics pipeline that integrates scATAC-seq data with other allosteric data, such as single-cell RNA sequencing (scRNA-seq), enabling researchers to discover links between chromatin accessibility, gene expression, and epigenetic modifications.

Applications of Plant scATAC-seq Analysis

• Identification of cell-type clusters.
• Characterization of plant cell type transcription factor motifs.
• Chromatin accessibility trajectory.
• Single-cell chromatin accessibility kinetics in response to heat stress.

Lifeasible is leading the way in providing integrated bioinformatics services for plant scATAC-seq analysis with its expertise, advanced infrastructure, and customized solutions. By leveraging our services, we can unlock the potential of scATAC-seq data to gain valuable information on plant biology, development, and environmental responses. If you are interested in our services or have some questions, please feel free to contact us or make an online inquiry.

Reference

1. Feng D, Liang Z, Wang Y, et al. Chromatin accessibility illuminates single-cell regulatory dynamics of rice root tips[J]. BMC biology, 2022, 20(1): 274.

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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)
• Single-cell Solutions for Plant Research