Small RNA Sequencing
Technical Information
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Small RNAs have emerged as important regulators in recent years. Small RNAs have significant functions in many cellular processes including development, cell differentiation and apoptosis, and have been implicated in many diseases. BGI’s small RNA sequencing and bioinformatics analysis services provide reliable detection and profiling of small RNAs rapidly and cost effectively.
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  1. Detection of virtually all small RNAs, repeat associated small RNAs, and degraded tags of exons and introns
  2. Wide range of transcript detection from two to several hundred thousand copies
  3. Detection of known miRNAs; prediction and detection of novel miRNAs
  4. Target gene prediction and function annotation
  5. High throughput reads: more than 8 million per single-pass sequencing
  6. High resolution: capable of discriminating single-base difference

Customer Testimonials:

"BGI offered a good price and the shortest turnaround time… The advanced bioinformatics service helped a lot in the data evaluation… During the process and even after finishing the project, the staff always responded quickly to our questions. The data allowed us to discover several differentially expressed miRNA and also novel miRNAs… BGI provides a world-class service and we will continue our project with their help, sequencing another 20 miRNA libraries” Dr. Marcelo Menossi, University of Campinas

MicroRNA Expression Signatures of Bladder Cancer Revealed by Deep Sequencing. PLoS One. 28 Mar 2011. 6(3):e18286.

MicroRNAs (miRNAs) are a class of small noncoding RNAs that regulate gene expression. They are aberrantly expressed in many types of cancers. In this study, we determined the genome-wide miRNA profiles in bladder urothelial carcinoma by deep sequencing. We detected 656 differentially expressed known human miRNAs and miRNA antisense sequences (miRNA*s) in nine bladder urothelial carcinoma patients by deep sequencing. Many miRNAs and miRNA*s were significantly upregulated or downregulated in bladder urothelial carcinoma compared to matched histologically normal urothelium.

Characterization of microRNAs in Serum: a Novel Class of Biomarkers for Diagnosis of Cancer and Other Diseases. Cell Res. 18 Oct 2008: 997–1006.

Dysregulated expression of microRNAs (miRNAs) in various tissues has been associated with a variety of diseases, including cancers. Here we demonstrate that miRNAs are present in the serum and plasma of humans and other animals such as mice, rats, bovine fetuses, calves, and horses. The levels of miRNAs in serum are stable, reproducible, and consistent among individuals of the same species. Employing Solexa, we sequenced all serum miRNAs of healthy Chinese subjects and found over 100 and 91 serum miRNAs in male and female subjects, respectively. We also identified specific expression patterns of serum miRNAs for lung cancer, colorectal cancer, and diabetes, providing evidence that serum miRNAs contain fingerprints for various diseases.

Bioinformatics Analysis:

Standard Bioinformatics Analysis

  1. Remove adaptors, low-quality tags, as well as contaminants to generate clean reads
  2. Summarize the length distribution of small RNAs
  3. Analyze common and specific sequences between two samples
  4. Explore small RNA distribution across the selected genome
  5. Identify rRNAs, tRNAs, snRNAs, etc. by aligning to Rfam and Genbank databases
  6. Identify repeat-associated small RNAs
  7. Identify degraded fragments of mRNAs
  8. Identify known miRNAs by aligning to a designated part of miRBase
  9. Annotate small RNAs into several categories based on priority
  10. Predict novel miRNAs and their secondary structures by Mireap from unannotated small RNAs
  11. Analyze the expression pattern of known miRNAs
  12. Perform family analysis of known miRNAs

Advanced Bioinformatics Analysis

  1. Differential expression analysis of miRNAs
  2. Target gene prediction of miRNAs
  3. Target gene GO annotation and KEGG pathway analysis of miRNA
  4. Base editing analysis of miRNA

Custom Bioinformatics Analysis

  1. We can also perform other customized analyses to meet the requirements of specific projects.

Sample Requirements:

  1. Sample condition: Integrated total RNA samples. Avoid protein contamination during RNA isolation.
  2. Sample quantity:
    1. General requirements: total RNA ≥10 μg
    2. For plasma/serum or samples used in Co-IP: total RNA ≥100 ng (≥ 5mL for serum sample)
    3. For < 200 nt small RNA isolated from mirVana™ miRNA Isolation Kit: RNA ≥1 μg
  3. Sample concentration:
    General requirements: concentration ≥200ng/μL
    For plasma/serum or samples used in Co-IP: concentration ≥ 5ng/μL
    For < 200 nt small RNA isolated from mirVana™ miRNA Isolation Kit: concentration ≥20 ng/μL
  4. Sample purity: OD260/280 = 1.8-2.2, OD260/230 ≥2.0, for eukaryote except insect 28S:18S ≥1.5, RIN ≥8.0

Turnaround Time:

The standard turnaround time for the workflow (above) is 30 business days.

Completion Indicator:

The completion is indicated by the number of the clean reads. Goals are individualized to each project.