Bovine ATAC-Seq

Bovines are far more genetically similar to humans than rats. This also means that bovines can be used as an alternative to laboratory rats as animal models for studying human diseases. With the completion of whole genome sequencing in cattle, there is a growing need for higher-level sequencing technologies for biological scientists. ATAC-seq, a novel technique for studying open chromatin, uses Tn5 transposase to access and cleave bare DNA, thereby obtaining information on accessible nuclear chromatin regions in cattle. In combination with RNA-seq, all actively transcribed regulatory sequences can be analyzed, which provides an important guide for studying transcription factors.

More and more scientists hope to use ATAC-seq to breed new breeds of bovine with better meat quality or more milk production, or to study the immune response regulatory pathways, mutational processes of disease-related genes, cell damage repair pathways, gene regulatory networks, etc. in bovine.

Lifeasible, a biotechnology company active in the field of sequencing, has been dedicated to providing bovine ATAC-Seq solutions to the satisfaction of customers engaged in related research for many years. Our technical services analyze the mechanisms of gene expression regulation from the perspective of chromatin conformation, and screen and identify vital regulatory elements.

Our Bovine ATAC-Seq Service Content

• Analysis of accessible chromatin in bronchial lymph nodes of cows Infected with the bovine respiratory syncytial virus (BRSV) by ATAC-seq

BRSV is one of the major pathogens causing bovine respiratory disease (BRD). We used BRSV to infect healthy cows with BRD and then used ATAC-seq to identify open chromatin regions of DNA in the bronchial lymphocytes of cows and analyze them in comparison with those of healthy calves. Genes that may be involved in the immune response induced by BRSV infection were identified, and this genetic information can guide cows' breeding.

Figure 1. Principal component plot of bronchial lymph node ATAC-seq regions of accessible chromatin data. (Johnston, D, et al. 2021)

• Using ATAC-seq to identify key genes regulating skeletal muscle development in bovine

The growth, development, and genetic characteristics of skeletal muscle are essential for beef yield and quality. The growth and development of skeletal muscle are regulated by a combination of regulatory factors. To explore this process, we combined ATAC-seq and RNA-seq to detect gene specifically expressed in skeletal muscle. We identified 54 key regulatory genes for skeletal muscle development, providing fundamental data to study the molecular mechanisms regulating mammal muscle development.

Figure 2. The landscape of genomic chromatin accessibility as analyzed by ATAC-seq. (Wang, J, et al. 2022)

• Using ATAC-seq technology to analyze the landscape of accessible chromatin in bovine oocytes and early embryos

We examined chromatin in bovine oocytes and early embryos using ATAC-seq technology, and the analysis yielded a genome-wide accessible chromatin map. Through differential analysis, we revealed critical features of chromatin landscape and epigenetic reprogramming during bovine preimplantation embryonic development.

Figure 3. Accessible chromatin landscape in bovine oocytes and early embryos as analyzed by ATAC-seq. (Ming, H, et al. 2021)

Technical Route of Bovine 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's animal-oriented sequencing technology platform provides scalable bovine ATAC-Seq services to customers worldwide. Our extensive project experience and quality project services ensure excellence every step of the way. Please feel free to contact us with questions, inquiries, or collaborations.