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RNA-SEQ (Quantification)

BGISEQ Based Service

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An Accessible, Cost Effective Sequencing Solution to Enable Rapid Discovery with Industry Leading Turnaround Times.


Service Description

It has been well documented in the literature that RNA sequencing presents a viable alternative to microarray-based Gene Expression analysis, and offers distinct benefits in sensitivity and dynamic range without the inherent bias present in microarrays (1).

The higher cost of NGS has prevented routine adoption of RNA sequencing, until now. BGI is proud to introduce Gene Expression Sequencing Services, with all the benefits from NGS data, but at a cost that is comparable to that of microarrays.

Confidence: Great correlation with microarray data.
Higher performance: Higher sensitivity and greater dynamic range.
More data: From clean FASTQ data to expression bioinformatics.
Lasting data: Analyze, Re-analyze your data as new insights develop.
Flexibility: Works for any species and with various sample types.
Cost effective: Now available at a lower price than microarray analysis.

Sequencing Service Specification

The BGI Gene Expression Sequencing Service will be performed with the BGISEQ-500 sequencing system, featuring cPAS and DNA Nanoballs (DNB) technology for superior data quality (2).

Sequencing Details

  • 50bp Single-end sequencing reads
  • Standard output 20 Million reads per sample
  • Clean filtered sequencing data delivered in standard FASTQ file format
  • Customized Gene Expression bioinformatics analysis
  • Cloud-based data storage and delivery system
    Turn Around Time:
  • Typical 25 working days from sample QC acceptance to final data delivery

Expedited services are available, contact your local BGI specialist for details

Project Workflow

We care for your samples from the start through to the result reporting. Highly experienced laboratory professionals follow strict quality procedures to ensure high quality results.

Gene_Expression_Sequencing_Workflow-01

 

Data Analysis

In addition to clean data output, BGI offers a range of standard and customized bioinformatics pipelines for your RNA-Seq (Quantification) Gene Expression Sequencing project.

Reports and output data files are delivered in industry standard FASTQ, BAM. Excel file formats with publication-ready tables and figures.

Graphic2

Gene_Expression_Sequencing_Analysis-01

Gene Expression Sequencing Performance 

qPCR remains the recognized gold standard for Gene Expression. The plots below show the correlation of BGISEQ-500 Gene Expression Sequencing data and Affymetrix microarray data with TaqMan qPCR data.

Microarray and qPCR data was generated as part of a FDA multi-site Microarray QC study (3), in which expression data of Human Brain Reference RNA (HBRR) and Universal Human Reference RNA (UHRR) samples were quantified and compared. These scatter plots compare the log ratio of differential expression values. The log ratio value is each gene’s log2 (HBRR/UHRR).

Graphic1

Gene Expression Sequencing offers superior sensitivity compared to microarrays.

With microarray data from the same Microarray QC study (3), this Venn-diagram compares detected gene numbers of several microarray products from a UHRR sample. BGISEQ-500 Gene Expression Sequencing data from the same reference sample has been added for comparison.

The results demonstrate the sensitivity of BGISEQ-500 Gene Expression Sequencing that identified 19,675 genes in the sample, of which 3,702 or 18% were unique genes that were not identified by the microarray methods.

Graphic3

Sample Requirements

We can process RNA samples of human, plant, fungi, rat, mice and other species, with the following general requirements:

Graphic4

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References

1 Comparison of RNA-Seq and Microarray in Transcriptome Pro ling of Activated T Cells

Shanrong Zhao, Wai-Ping Fung-Leung, Anton Bittner, Karen Ngo, Xuejun Liu PLoS One(2014) 9(1):e78644 doi: 10.1371/journal.pone.0078644 http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0078644

2 Human genome sequencing using unchained base reads on self-assembling DNA nanoarrays

Drmanac R, Sparks AB, Callow MJ, Halpern AL, Burns NL, Kermani BG, Carnevali P, Nazarenko I, Nilsen GB, Yeung G, et al.
Science(2010) 327(5961):78–81 doi:10.1126/science.1181498 http://science.sciencemag.org/content/327/5961/78.full

3 The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements
MAQC Consortium
NATURE Biotechnology Volume 24 Number 9 September 2006; doi:10.1038/nbt1239 https://www.ncbi.nlm.nih.gov/pubmed/16964229

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HiSeq Based Service

An Accessible, Cost Effective Sequencing Solution to Enable Rapid Discovery with Industry Leading Turnaround Times.


Service Description

RNA-Seq (Quantification) is used to reveal the presence and quantity of RNA in a biological sample under specific conditions. Compared to hybridization-based RNA quanti cation method such as microarray, sequencing-based transcriptome detection can quantify gene expression with low background, high accuracy and high levels of reproducibility within a large dynamic range. RNA-Seq (Quantitation) allows the entire transcriptome to be surveyed in a very high-throughput and quantitative manner at single-base resolution.

Sequencing Service Specification 

BGI RNA-Sequencing (Quantification) services are executed with the Illumina HiSeq 4000 or with the BGISEQ-500 sequencing system.

Sequencing Details

  • 50bp Single-end sequencing
  • Raw data and bioinformatics analysis are available in standard file formats
  • Advanced and custom bioinformatics data analysis
  • Cloud-based data storage and delivery system
  • ≥20 Million reads per sample recommended

Turn Around Time

  • Typical 30 working days from sample QC acceptance to ltered raw data availability
  • Expedited services are available, contact your local BGI specialist for details

Sample Requirements

We can process your total RNA, Blood, Cell line, FFPE, Fresh Frozen tissue and Single Cell samples from a variety of species, with the following general requirements:

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BGI RNA Seq (quantification) sample requirements

Project Workflow

We care for your samples from the start through to the result reporting. Highly experienced laboratory professionals follow strict quality procedures to ensure the integrity of your results.

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BGI RNA seq (quantification) project workflow

Data Analysis

In addition to raw data output, BGI offers a range of standard and customized bioinformatics pipelines for your RNA-Seq (Quantification) sequencing project.

Reports and output data ies are delivered in industry standard le formats: FASTQ, BAM, FPKM calculation and Excel.

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BGI RNA seq (quantification) data analysis

Resources
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Don’t hesitate to contact us to request a quote or to talk more about your requirements and how we can support your needs.


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Customer Testimonial

“As the principal investigator on two sequencing projects that are pushing the state-of-the-art (viral discovery using metagenomic sequencing and phylogenomic analysis of 1000 plant species), I cannot expect everything to work on the first iteration but I do expect my sequencing provider to work together with me to correct whatever went wrong regardless of whose fault it was. BGI-Shenzhen does that admirably.” – Dr. GaneKa-Shu Wong, Professor and iCORE Chair in Biosystems Informatics Department of Biological Sciences, University of Alberta
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