Degradome sequencing (Degradome-Seq), also referred to as parallel analysis of RNA ends (PARE), a modified 5′-rapid amplification of cDNA ends (RACE) with high-throughput next-gen sequencing method. Degradome sequencing provides a comprehensive means of analyzing patterns of RNA degradation.
Degradome sequencing has been use to identify microRNA (miRNA) cleavage sites, because miRNAs can cause endonucleolytic cleavage of mRNA by extensive and often perfect complementarity to mRNAs. Degradome sequencing has revealed many known and novel plant miRNA (siRNA) targets.
- In plants, microRNAs tend to cause cleavage of their targets at the position between nucleotides 10 and 11 of the microRNA
- Next-Gen sequencing of the 5’ ends of RNA degradation products allows identification of over-represented 5’ ends (microRNA cleavage sites)
- Matching cleavage sites to known microRNA sequences links microRNAs to their targets
Our Comprehensive Service
LC Sciences provides a a one-stop solution (i.e. from sample to data) degradome sequencing service using the Illumina next-generation sequencing technology which enables comprehensive coverage, highly sensitive and specific profiling of miRNAs and mRNA degradome in your total RNA sample.
This service is comprehensive – from sample to data, providing advanced technology and years of experience in efficient discovery and profiling of RNAs.
Our comprehensive profiling service includes:
- Sample QC
- Library preparation (includes both small RNA and degradome library prep)
- High-throughput sequencing (RNA-Seq method, Illumina Next-Gen sequencing technology)
- Bioinformatics analysis
- Customer data report
Data Analysis / Results
For each sample analyzed, the customer receives:
- Assessment of sequencing and quality filtering of raw reads
- Raw sequencing data – up to 30M 35 bp single-end reads – either FASTA-A or FASTA-Q files with base-calling quality scores
- LC Sciences quality filtered data reduced to mappable reads, a list of unique sequences and their copy numbers
- Custom construction of reference database(s) – miRBase, genome, etc and mapping of all quality reads
- Alignment, classification, & functional annotation of all mapped reads
- Identification of rRNAs, tRNAs, snRNAs, snoRNAs, polyN and other non-coding RNAs
- Prediction of possible novel miRs
- Biostatistical analysis – expression analysis, multi-parameter data analysis, length distribution, transcript copy number comparisons, etc
- Distribution of degradation fragments on selected region of genome
- Identification of target mRNAs
- Statistical summary of mRNA degradation sites
- Identification of degradation mRNA related microRNAs from miRBase (Results will be shown in a target plot diagram.)
- Customer data report – includes a summary of methods and all statistic analysis