Ribo seq Technical Services

Ribo seq Technical Services

technical principle

Proteins are the main carriers of life activities, and translation regulation is an important regulatory mechanism within cells. Translation is the process in which ribosomes read mRNA templates to guide protein synthesis and is a crucial step in gene expression. The process of translation is strictly regulated, and many diseases are related to translation abnormalities, such as neurodegenerative diseases, anemia, and developmental disorders. Although the structure and function of ribosomes have been studied thoroughly, further research is needed on the regulatory mechanisms of translation processes.

Ribosome profiling,Ribo-seq）Can detect the translation status in the body in detail.Ribo-seqThe core of the technology is to identify mRNA that binds to ribosomes and approximately 30 nucleotides that are being translated. Sequencing mRNA fragments bound to ribosomes can accurately record the position of ribosomes during translation. Integrate transcriptome withRibo-seqJoint data analysis can calculate the synthesis rate of proteins.

Technical Features

Ribo-seqCan reveal the time, location, and position of protein synthesis, which proteins are being synthesized, and the regulatory mechanisms of protein synthesis.Ribo-seqBuilt a bridge between transcriptomics and proteomics, it has been widely applied in animal, plant, and microbial research to reveal the regulatory mechanisms of growth and development, morphogenesis, disease occurrence, and stress response.

Application Direction

Ribo-seqApplied to study the translation activity of transcripts, identify translation start sites, ORF positions, and protein translation regulatory mechanisms.

Ribo-seqTechnology has been widely applied in the research of animals, plants, and microorganisms to reveal the regulatory mechanisms of growth and development, morphogenesis, disease occurrence, and stress response. In short,Ribo-seqIt can detect the translation status of proteins at the genomic level, obtain information on the mRNA sequence being translated, and analyze the translation regulatory mechanism.

Advantages of Lanjing Kexin

The experimental cycle is fast, the quality is high, and the results are stable and reliable.

Rich species experience.

Ribo seq Technical ServicesExperimental Procedure

Analyze content

Standard bioinformatics analysis

(1) Raw data filtering and sequencing quality assessment

(2) Compare and remove ribosomal RNA, tRNA, sRNA, etc

(3) Reads length distribution statistics and length filtering

(4) Comparing reference genomes

(5) Sequencing saturation analysis

(6) Distribution statistics and classification of RF on the genome

(7) Three base rhythm analysis

(8) Translation gene statistics and expression level analysis

(9) Sample Relationship Analysis

(10) Analysis of intergroup differential translation genes

(11) GO and KEGG functional enrichment analysis of differentially translated genes

Ribo-seqJoint analysis with RNA seq

(1) Translation efficiency calculation

(2) Correlation analysis between Ribo seq and RNA seq

(3) Correlation analysis between translation efficiency and transcription level

Analysis process

experimental case

Sample submission requirements

(1) Cell samples: It is recommended to send 5 × 106-1 × 107 samples.

(2) Animal tissue samples: It is recommended to send a sample size of ≥ 300 mg.

(3) Plant tissue samples: It is recommended to send a sample size of ≥ 500 mg.

Sample grouping

At least 2 sets of samples, including control group and experimental group, with a recommended sample size of 3 Vs 3.

References

BrarGA,WeissmanJS. Ribosome profiling reveals the what, when, where and how of protein synthesis. Nat Rev Mol Cell Biol. 2015. 16(11):651-664.

ChongC, Coukos G, Bassani-Sternberg M. Identification of tumor antigens with immunopeptidomics. Nat Biotechnol. 2022. 40(2):175-188.

FreminBJ, Nicolaou C, Bhatt AS. Simultaneous ribosome profiling of hundreds of microbes from the human microbiome. Nat Protoc. 2021. 16(10):4676-4691.

IngoliaNT, Brar GA, Rouskin S, McGeachy AM, Weissman JS. The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments. Nat Protoc. 2012. 7(8):1534-1550.

IngoliaNT, Ghaemmaghami S, Newman JR, Weissman JS. Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science. 2009. 324(5924):218-223.

JuntawongP, Girke T, Bazin J, Bailey-Serres J. Translational dynamics revealed by genome-wide profiling of ribosome footprints in Arabidopsis. Proc Natl Acad Sci U S A. 2014. 111(1):E203-212.

SawyerEB, Cortes T. Ribosome profiling enhances understanding of mycobacterial translation. Front Microbiol. 2022. 13:976550.

Xiang Y, Huang W, Tan L, Chen T, He Y, Irving PS, Weeks KM, Zhang QC, Dong X. Pervasive downstream RNA hairpins dynamically dictate start-codon selection. Nature. 2023. 621(7978):423-430.

Xu G, Greene GH, Yoo H, Liu L, Marqués J, Motley J, Dong X. Global translational reprogramming is a fundamental layer of immune regulation in plants. Nature. 2017. 545(7655):487-490.