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Total RNA-seq

YanWhole-transcriptome analysis with total RNA sequencing (RNA-Seq) detects coding plus multiple forms of noncoding RNA. Total RNA-Seq can accurately measure gene and transcript abundance and identify known and novel features of the transcriptome.

For library preparation recommendations based on species, please see the below chart for details.

Species Library Preparation
Human/Mouse/Rat TruSeq Ribo-Zero-Gold and Kapa Ribo-Erase
Individual species depletions
  • Tecan Genomics Ovation Universal RNAseq with any deplete
  • Nugen Solo
  • Nugen Trio

For low input material, the HTSF typically recommends Tecan Genomics SOLO or Trio, which can be done with any depletion for ribosomal depletion.

General sequencing platform and pooling recommendations can be found below:

Service Samples per Pool Platform Cycles
Total RNAseq 24 NovaSeq S4 2×150
96 2×50
38 NovaSeq S2
16 NovaSeq S1
8 NovaSeq SP
3 HiSeq 4000
*NOTE: Anticipated yield of 100 million clusters (200 million reads) per library


Library StaffmRNA sequencing (mRNA-Seq) has rapidly become the method of choice for analyzing the transcriptomes of disease states, of biological processes, and across a wide range of study designs. mRNA-Seq can identify both known and novel transcript isoforms, gene fusions, and other features as well as allele-specific expression. mRNA-Seq delivers a complete view of the coding transcriptome that is not restricted by the filter of prior knowledge.

There are a variety of approaches to mRNA sequencing. Therefore, the best approach will depend on your needs.
ScicloneTypically, the HTSF recommends the following library preparation methods:

  • Kapa mRNA stranded
  • Takara Smarter + Nextera XT for low input material
  • Nugen mRNA can also be done by request.

Sequencing and pooling recommendations can be found in the table below:

Services Samples per Pool Platform Cycles
mRNA-Seq 198 NovaSeq S4 2×50
76 NovaSeq S2
32 NovaSeq S1
16 NovaSeq SP
6 HiSeq 4000
*NOTE: Anticipated yield of 50 million clusters (100 million reads) per library

Small RNA sequencing

HongweiMicroRNA sequencing (miRNA-seq), a type of RNA-Seq, is the use of next-generation sequencing to sequence microRNAs, also called miRNAs. miRNA-seq differs from other forms of RNA-seq in that input material is typically enriched for small RNAs. miRNA-seq allows researchers to examine tissue-specific expression patterns, disease associations, and isoforms of miRNAs, and to discover previously uncharacterized miRNAs.

Like other miRNA profiling technologies, miRNA-Seq has both advantages (sequence-independence, coverage) and disadvantages (high cost, infrastructure requirements, run length, and potential artifacts).

Preferred library preparation kits for this service include:

  • BioO NextFlex

Sequencing and pooling recommendations can be found in the table below:

Service Samples per Pool Platform Cycle
Small RNA-seq 48 NextSeq 2000 Single End/50x
*NOTE: Anticipated yield of 20 million reads/clusters per library

Relevant RNA Services Forms and Guides

HTSF Sample Preparation Requirement Guide
Illumina Platform Comparison and Specification Table
NovaSeq Requirements
NovaSeq White Paper
Approved Containers Information