Degradome Profiling (Degradome Sequencing)

Overview Features Workflow & Data Analysis Requirements Demo Case Study FAQ Resources Inquiry

Degradome sequencing is a next-generation sequencing (NGS)-based method to comprehensively detect microRNA, a class of endogenous non-coding small RNA with of about 22 nt in length. These small fragments accumulate stably in cells, some of which may participate in the regulation of alternative splicing or protein translation. We provide one-stop Degradome sequencing services to help you research microRNA in depth.


MicroRNA (miRNA) is a type of endogenous non-coding small RNA with a length of about 22 nt, which is widely present in animals, plants, viruses, and other organisms. Studies have shown that miRNAs are involved in various biological processes of cell proliferation, apoptosis, differentiation, metabolism, tumor, growth and development, and stress response in animals and plants. miRNA achieves its important biological functions through the expression of target genes (mRNA) regulated at the post-transcriptional level. Therefore, identifying mRNA regulated by miRNA is the key to explaining the complex regulatory mechanisms of miRNAs. We provide comprehensive degradome sequencing to help customers in-depth study of the role of non-coding RNAs. The technology is mainly aimed at sequencing miRNA-mediated shearing and degrading fragments, screening target genes of miRNA from experiments, and combining the advantages of bioinformatics analysis to determine the precise pairing information between degraded fragments and miRNA. Meantime, it can accurately and efficiently screen out miRNA target genes from cells or tissues, and provide accurate and efficient screening methods for studying the relationship between miRNAs and their corresponding target genes. Degradome Sequencing promotes the functional research of miRNAs, can precisely and efficiently screen miRNA target genes from cells or tissues, and provide accurate and efficient screening methods for studying the relationship between miRNAs and their corresponding target genes.

Integrative Transcriptome-Small RNA- Degradome sequencing Solution

Our solution employs a multiomics approach, integrating transcriptome, small RNA sequencing, and degradome profiling to unravel intricate gene regulatory networks. The miRNA sequences utilized for degradome analysis are derived from small RNA sequencing, while the comparative database comprises sequences spliced by transcriptome sequencing. This method unveils the intricate relationships between miRNAs and target genes, providing a clear miRNA-target gene network regulation map.

This map succinctly illustrates how miRNAs regulate multiple target genes, and conversely, how the same target gene can be regulated by multiple miRNAs. The synthesis and analysis of these three datasets uncover the nuanced regulatory mechanisms underlying the gene expression process, offering valuable insights into the intricate network of genetic regulation.


High Throughput High Accuracy High Repeatability One-stop Service
Obtain more than 10 million sequence information in one sequencing. Accurate counts of copies from a few to hundreds of thousands. Deep sequencing ensures the randomness of detection and does not require technical repetition. Provides one-stop service for library construction, sequencing, sample QC and data analysis.

Project Workflow

Sample Preparation

1. Sample Preparation

RNA purification;
quality assessment and quantification.

Library Preparation

2. Library Preparation

Size selection;
strand-specific cDNA libraries.


3. Sequencing

Illumina HiSeq;
PE 50/75/100/150.

Data Analysis

4. Data Analysis

Visualize and preprocess results, and perform custom bioinformatics analysis.

Bioinformatics Analysis Pipeline

Degradome Profiling

In-depth data analysis:

  • Reference-based mapping
  • Sequence depth statistics of mRNA
  • Predict target genes of known miRNAs
  • Degradation site analysis
  • Classification annotation of non-coding RNA
  • Identification of known and novel non-coding RNAs
  • GO and KEGG pathway analysis
  • Clustering analysis and enrichment analysis

Sample Requirements

RNA sample quantity ≥ 20 ug.
1.8 ≤ OD260/280 ≤ 2.2, OD260/230 ≥ 1.0, 28S:18S ≥ 1.5, RIN ≥ 7.0.
Please make sure that the RNA is not significantly degraded.

Sample storage: RNA can be dissolved in ethanol or RNA-free ultra-pure water and stored at -80°C. RNA should avoid repeated freezing and thawing.

Shipping Method: When shipping RNA samples, the RNA sample is stored in a 1.5 mL Eppendorf tube, sealed with sealing film. Shipments are generally recommended to contain 5-10 pounds of dry ice per 24 hours.

Deliverable: FastQ, BAM, coverage summary, QC report, custom bioinformatics analysis.

Demo Results

Differential miRNA clustering heatmapDifferential miRNA clustering heatmap

miRNAs and target genes interactionsmiRNAs and target genes interactions

GO enrichmentGO enrichment

Case Studies



  1. Yongping Zhao, Zhenhua Xu, Qiaocheng Mo, et al. Combined small RNA and degradome sequencing reveals novel miRNAs and their targets in response to low nitrate availability in maize. Ann Bot, 2013, 8, 112(3): 633-642.
  2. Xiyan Yang, Lichen Wang, Daojun Yuan, et al. Small RNA and degradome sequencing reveal complex miRNA regulation during cotton somatic embryogenesis. J Exp Bot, 2013, 4, 64(6): 1521-1536.
  3. Dongliang Yu, Min Xu, Hidetaka Ito, et al. Tracking microRNA Processing Signals by Degradome Sequencing Data Analysis. Front Genet, 2018, 9: 546.
* For Research Use Only. Not for use in diagnostic procedures.

Research Areas
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