Leading Edge Genomic Services & Solutions

mRNA-Seq

Service Overview
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RNA Sequencing ServiceCompared with microarray analysis, mRNA sequencing (RNA-Seq) provides a more precise and complete snapshot of the transcriptome and enables the identification of novel transcripts, alternative splicing and gene fusion events. RNA-Seq also provides an alternative and affordable approach for gene expression quantification and differential gene expression analysis among groups of samples. It is widely used in disease research, drug response research, pharmacokinetics, and personalized healthcare research.

Novogene offers complete solutions for transcriptome sequencing and RNA-Seq quantification using Illumina HiSeq 4000 platform with PE150bp sequencing strategy. The longer read length ensures superior data quality and accurate sequence assembly. Our experienced bioinformatians work closely with customers to provide standard and customized data analysis and publication ready results for species with and without a reference genome.

In addition to mRNA sequencing, we offer lncRNA, circular RNA, and small RNA sequencing services. Contact us to learn more.

The Novogene Advantage

  • Extensive experience with >30,000 samples successfully sequenced in over 5,000 completed projects and articles published on transcriptome sequencing results across different species.
  • Unsurpassed data quality with a guaranteed Q30 score ≥80% that exceeds Illumina’s official guarantee.
  • Comprehensive data analysis using widely accepted mainstream software and mature in-house pipeline to discover novel transcripts, differential expressions, and function annotations.
  • Free, powerful Novofinder software that enables Novogene customers to easily access and visualize data analysis results and annotations through a user-friendly interface.

Project Workflow

RNA Sequencing Service Project Workflow

Sequencing Strategy

  • 250~300 bp insert cDNA library
  • HiSeq platform, paired-end 150 bp (Transcriptome sequencing service)
  • HiSeq platform, single-end 50 bp (RNA-Seq quantification service)

Data Quality Guarantee

  • Our data quality guarantee, as measured by the percentage of bases with a sequencing quality score above Q30 (PE 150, ≥80%; SE 50, ≥90%), exceeds Illumina’s official guarantee (PE 150, ≥75%; SE 50, ≥80%). See examples of our high quality data.

Sample Requirements

For both services:
  • Total RNA amount: ≥ 1.0 μg; RNA concentration: ≥ 50 ng/μl (For human and mouse, 200 ng could be accepted with risk.)
  • RIN value ≥ 6.3 for plants and fungi; RIN value ≥ 6.8 for animals
  • OD260/280 ≥ 2.0, OD260/230 ≥ 2.0, without degradation and DNA contamination
  • FFPE sample: > 10 scrolls or slides. Samples should be tested as pre-qualified by gel electrophoresis before sample submission.

Turnaround Time

  • Within 15 working days from verification of sample quality without data analysis
  • The turnaround for data analysis is project dependent.

Recommended Sequencing Depth

  • ≥ 20 M reads

Analysis Pipeline

Transcriptome sequencing service analysis pipeline
Pipeline for RNA Sequencing Service Transcriptome
RNA-seq quantification service analysis pipeline
Pipeline for RNA Sequencing Service Quantification
Table. Representative data quality results of Novogene's mRNA sequencing service (PE150)
Sample Name# Of Raw reads# Of Clean readsClean basesError Rate (%)Q 20 (%)Q 30(%)GC Content (%)
a61857270582723668.74G0.0296.5591.8249.63
b63461444596344068.95G0.0296.6691.9747.74
c54854516511786747.68G0.0296.4691.5649.55
d54204202521915867.83G0.0296.4691.5351.54
e62043078597147528.96G0.0296.3191.1851.27
f760304707281341210.92G0.0296.3891.4053.36

Project Example

The following study utilized Novogene's expert mRNA-Seq services.

mRNA and small RNA transcriptomes reveal insights into dynamic homoeolog regulation of allopolyploid heterosis in nascent hexaploid wheat
The Plant Cell, 26:1878-1900 (2014)

As published online in The Plant Cell, Novogene, in cooperation with the Chinese Academy of Agriculture Sciences, reported that mRNA and small RNA transcriptomes provide insights into small RNA–mediated dynamic homoeolog regulation mechanisms that may contribute to heterosis in nascent hexaploid wheat. Expression level dominance, in which genes exhibit the expression levels of a dominant subgenome, was observed for a large number of genes associated with development and adaptation. Results also suggested that microRNAs and small interfering RNAs contribute to the differential gene expression patterns observed in hybrid progeny. The findings advanced our understanding of the regulation of key agronomic traits in a major food crop.

mRNA chart

Figure. Hierarchical clustering of microRNAs that exhibit (left panel) nonadditive expression and (right panel) parental patterns of expression level dominance.

Examples of Publications Using Novogene’s Expertise

JournalTitle
Nature Structural & Molecular Biology, 20, 1131-1139 (2013)Single-cell RNA-seq profiling of human preimplantation embryos and embryonic stem cells.
Genome Research, 24:1765 (2014)RNA-seq of 272 gliomas revealed a novel, recurrent PTPRZ1-MET fusion transcript in secondary glioblastomas.
Nature Communications, 6:6239 (2015)Integration of Hippo signalling and the unfolded protein response to restrain liver overgrowth and tumorigenesis.
Cell Stem Cell, 18:495 (2016) The RNA-seq approach to discriminate gene expression profiles in response to melatonin on cucumber lateral root formation.
Genome Research, 26:499 (2016) Genome-wide A-to-I RNA editing in fungi independent of ADAR enzymes.
Nature, 533, 487-492 (2016)Tracing haematopoietic stem cell formation at single-cell resolution.
New Phytologist, 11:12 (2016)Exploring key cellular processes and candidate genes regulating the primary thickening growth of Moso underground shoots.
New Phytologist, 213:275 (2017)ABNORMAL VASCULAR BUNDLES regulates cell proliferation and procambium cell establishment during aerial organ development in rice.
  Whole Genome Sequencing on HiSeq X (Human/ Animal/ Plant)
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  mRNA-Seq
  LncRNA Sequencing
  Small RNA Sequencing
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  Animal & Plant Re-Sequencing
  Genotyping by Sequencing
  de novo Sequencing
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