Degradome Sequencing

Degradome sis a modified version of 5'-equencing (Degradome-Seq), also referred to as parallel analysis of RNA ends (PARE), Rapid Amplification of cDNA Ends (RACE) using high-throughput, deep sequencing method using as Illumina's SBS technology. Degradome sequencing provides a comprehensive means of analyzing patterns of RNA degradation.

Degradome sequencing has been used to identify: microRNA (miRNA) cleavage sites, because miRNAs can cause endonucleolytic cleavage of mRNA by extensive and often perfect complementarity to mRNAs. Degradome sequencing reveals many known and miRNA (siRNA) targets nd miRNA-dervied cleavages.

Sequencing using HiSEQ 2500
Single end 50 base Read length
40 Million Paired-end Reads
Standard Bioinformatics Included

Standard Degradome Bioinformatics:
Quality Control

1. Raw data QC.
2. Removal of low quality reads and trimming of Low quality bases.
3. Adaptor trimming.

Degradome Analysis:

1. CleaveLand (version: 4.3) will used to determine small RNA targets.
2. Input degradome sequences, small RNAs and an mRNA database.
3. Distribution of degradation fragments on selected region of genome.
4. Identification of target mRNAs.
5. Statistical summary of mRNA degradation sites.
6. Differential Gene expression: MA-Plot, Volcano Plots, heatmap. Identification of degradation mRNA related microRNAs from miRBase (Results will be shown in a target plot T-PLOT diagram.