RNA Sequencing Services at Ocean Ridge Biosciences

Ocean Ridge Biosciences (ORB) offers a full suite of RNA sequencing services which utilize Illumina instruments including the HiSeq 2500, HiSeq 4000, and the NextSeq 500. lllumina’s unique combination of error rates below 0.1%, paired-end read lengths of 50-250 nucleotides, quantities of up to 6.6 billion reads per sequencing run, and rapid run times of 1-3 days, together provide a powerful advantage for RNA profiling projects that cannot be matched by instrumentation from competitors. ORB staff are dedicated to providing customized laboratory and computational workflows that enable cost-effective and rapid production of informative data sets, leading to advances in biomarker discovery, drug discovery, and basic medical research for its clients.

Sample Handling and RNA Extraction

ORB is able to accept and extract RNA from a wide variety of biofluids, tissues and cell preparations. The company has extensive experience with difficult sample types such saliva, bone and feces. RNA extracted from frozen tissue or cells can be processed for both long and small RNA sequencing; whereas RNA extracted from biofluids, exosome preparations, and fixed tissues are better suited for profiling of small RNAs. ORB also accepts total RNA. View Table I for sample types which are suitable for ORB’s RNA sequencing workflow, and visit ORB’s general sample information page for details about sample types versus application, minimal mass, and guidelines for upstream sample handling.

Library preparation

ORB has developed standard operating protocols for a numerous commercial library preparation kits and is therefore able to handle a wide range of input RNA amounts, levels of degradation, and biological applications. For mRNA or long ncRNA sequencing, ORB can prepare libraries from a minimum of 30 pg of intact RNA or 500 pg of partially degraded RNA. For small RNA, we currently accept a minimum of 20 ng of RNA or 200 ul of standard biofluids such as plasma, serum, and cerebrospinal fluid. See the individual small and long RNA sequencing pages for more information.

Sequencing options

Sequencer, read-length, and depth are determined by balancing the requirements of the application versus cost and turn-around time. ORB's Illumina Sequencing page provides recommended sequencing configuration and instruments for several applications.

   Figure 1. HiSeq 4000 Sequencer.

   Figure 2. HiSeq 4000 patterned flow cells, Illumina Corp.

   Figure 3. Google cloud computing center, Alphabet.

Applications

ORB provides specific expertise in RNA extraction, library preparation, sequencing, and data processing in several focused areas as well as general RNA sequencing projects. Please visit the additional pages linked below for more information about each type of application or contact us to receive consultation by e-mail or phone.

Core
Applications



Long RNA Sequencing
Focused
Applications



Biofluid Profiling

Table I. Typical sample types suitable for long or small RNA analysis
Long or small RNA Small RNA only
  • Frozen or RNALater-preserved tissue

  • Cultured cell lysates

  • Buffy coat or PBMCs

  • Flow-sorted cells

  • Laser capture micro-dissected cells

  • Immuno-precipitated RNA

  • OCT-preserved tissue sections

  • FFPE tissue sections (mRNA profiling depends on quality of preservation)

  • Exosomes

  • Serum, Plasma, Lymph

  • Cerebral Spinal Fluid

  • Lavage and Synovial Fluid

  • Amniotic Fluid

  • Degraded RNA

  • FFPE tissue sections

  • Fixed cells
  • RNA prepared by HITS-CLIP or PAR-CLIP

 
Contact us to receive consultation by e-mail or phone regarding the best RNA sequencing strategy to achieve your research goals!