Rat ATAC-Seq

Almost all human genes associated with the disease can find counterparts in the rat genome. In contrast, rats are several times larger than mice and possess fewer stress responses, enabling better research on disease mechanisms, new drug evaluation, etc.

As epigenomic sequencing technology continues to be applied in rats, more epigenetic regulatory mechanisms are being elucidated. ATAC-seq technology can detect chromatin openings genome-wide in rats and obtain genome-wide information on possible protein binding sites, helping researchers to identify valuable transcriptional regulatory regions.

Lifeasible focuses on providing efficient and accurate sequencing services. Our professional high-throughput sequencing platform can provide quality basic data for disease mechanism research and drug discovery. We offer a wide range of rat ATAC-seq technology solutions that can effectively advance our clients' projects and help them explore the state of binding of various regulatory factors to open chromatin.

Our Rat ATAC-Seq Service Content

• Analysis of cell types, regulatory elements, and SNPs in rat skeletal muscle cells using ATAC-seq

We sequenced rat skeletal muscle-associated genes using single nucleus ATAC-seq (snATAC-seq) technology to map specific chromatin accessibility. Skeletal muscle cell types were identified by multi-omics analysis with sequencing results from human cells. Moreover, we identified SNPs, transcription factors, and target genes associated with diabetic signaling and further went through cell types to discover the relationship between cells and diseases.

Figure 1. Cell type-specific ATAC-seq peaks and the cell types, regulatory elements, and SNPs were analyzed. (Orchard, P et al. 2021)

• Chromatin accessibility analysis of rat adipose and muscle tissues

We have optimized the reproducibility of ATAC-seq analysis in adipocytes to enable rapid and accurate chromatin genomic analysis and transcription factor binding site discovery in rat adipose tissue. Our experimental data are highly reproducible, helping scientists to advance relevant exploratory research in adipose tissue.

Figure 2. Flow chart of chromatin accessibility analysis of rat adipose and muscle tissue using ATAC-seq. (Nair, V. D, et al. 2022)

• Analysis of gene expression in the peripheral nervous system in rat models of persistent pain using ATAC-seq

We used ATAC-seq technology to examine the transcriptional profile of genes involved in the peripheral nervous system in a rat model of chronic pain response and the epigenetic basis of chronic pain. Different pain models demonstrate changes in chromatin accessibility, providing a good idea for identifying pathways associated with pain response and facilitating scientists to identify regulatory elements that play an essential role in persistent pain.

Figure 3. Chromatin accessibility in rat DRG. (Stephens, K. E, et al. 2021)

Technical Route of Rat ATAC-Seq

Sample Requirements

• Cells: > 2 × 10⁵
• Tissue: 50 mg/serving
• Take cells in a good growth state for trypsin digestion counting to ensure cell viability of 85% or more.
• Resuspend the cells in the cryopreservation solution and add 80-100,000 cells per cryopreservation tube. (Basic freezing solution recipe: 50% FBS + 40% complete medium + 10% DMSO)

Please note: Ensure sufficient dry ice when transporting samples to avoid temperature rise to destroy cell activity.

Bioinformatics Analysis Content

• Raw data collation, filtering, and quality assessment
• Reference genome annotation collation and statistics
• Reference sequence alignment analysis
• Peak calling
• Peak-associated gene GO annotation
• KEGG annotation of Peak-related genes
• Sample-to-sample differential Peak analysis
• Differential Peak-related gene GO enrichment analysis
• Differential Peak-related gene KEGG pathway enrichment analysis
• Nucleosome localization
• Genome-wide chromatin open mapping

Lifeasible provides professional rat ATAC-seq services according to our client's needs. Our state-of-the-art laboratory facilities, well-established animal houses, and rigorous sequencing data management can ensure data stability between multiple batches, providing our clients with authentic and accurate data. We focus on saving our clients' time and effort, allowing them to focus on their most scientifically innovative work. Please feel free to contact us with questions, inquiries, or collaborations.