Small RNASeq

Different from transcriptomic RNA Sequencing,  small RNASeq detects shorter fragments of RNA by customized size selection.  This technology allows investigators to quantify miRNA and other small non-coding RNAs and characterize sequence variation. The CCCB can perform small RNA-Seq on either cellular or plasma (extracellular, circulating) RNA. These experiments are run on Single Read 50 cycle (SR50) flowcells, on either the HiSeq or the MiSeq. 

Sequencing Results

  • Raw Data:  Demultiplexed raw read in zipped fastq format
  • Quality Control Report: Sequence data quality assessment based on FastQC package including per-base read quality, over-represented sequences, and over-represented k-mers
  • Alignment File: Sequenced reads are aligned to a reference genome (hg19, mm10, rn4) using STAR algorithm to produce an aligned BAM file
  • Quantification:  Known miRNA will be quantified in the sample using the mirDeep2 algorithm, which produces count values for all known miRNA. 

Bioinformatics Support

Small RNASeq Analysis Pipeline is available upon request as described in sRNASeq Analysis,  We can also perform customized analysis to meet specific needs of your projects.

Required Sample Inputs

NEBNext smRNASeq (Plasma): 10ng isolated plasma RNA
NEBNext smRNASeq (Cellular): 100ng total RNA