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Ocean Ridge Biosciences

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Palm Beach Gardens, Florida, US

About Ocean Ridge Biosciences

Ocean Ridge Biosciences (ORB) is a growing life science company in the research tools sector of biotechnology. Our mission is to provide accurate, affordable, and information-rich genomic services to the Health Care and Life Science industries. We are headquartered in Palm Beach Gardens, Florida, near the geographic center of a rapidly developing Life Science Cluster. Demand for high quality genomic services is steadily increasing for both research and clinical applications. ORB is capitalizing on that growth due to our capability of providing these services at attractive pricing in combination with excellent customer service.

ORB' major industry partners include Microarrays Inc., the leader in probe deposition-based microarray technology, and Toxikon, a well-respected pre-clinical CRO with operations in the U.S. and Europe.

ORB staff recently coauthored studies appearing in the journals PNAS and Nature with scientists at The Scripps Research Institute in Jupiter Florida. ORB is also engaged in research collaborations with several academic institutes focused on biomarker discovery in disease areas such as neurodegeneration, cardiovascular disease, and emphysema. Our partners on these projects include research groups at Emory University, Roosevelt Hospital in New York, and the University of Miami. ORB is also developing a recently in-licensed technology for RNA sample analysis with potential research and diagnostic applications in oncology, inflammation, and neurology.

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Our Services (20)


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Biomarker Analysis

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Gene expression profiling Luminex®

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Luminex Multiplex Assays

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Luminex xMAP technology enables the profiling of up to 100 different analytes in a single multiplex reaction. Luminex Corp. has developed a standard set of 100 polystyrene microspheres, each imbedded with specific ratios of two different fluorecent dyes. The ratio of the two dyes gives each bead type a unique specific identification of that bead in a mixture of other beads. It is possible to design multiplexed protein profiling assays for the xMAP technology platform. Several hundred assay kits are already available.

In the typical xMAP cytokine assay, specific bead types are each assigned to a different cytokine and coupled to primary antibodies directed against unique cytokine molecules. The bead mixtures are incubated with serum or cell culture supernatants in filter plates. The beads are then washed and incubated successively with biotinylated antibodies against each cytokine and with streptavadin-phycoerythrin.

Mixtures of beads are injected in to the Luminex LX100 instrument, a modified flow-cytometer, wherein the type and levels of each analyte can be determined by laser-induced fluorescence.


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MicroRNA (miRNA) Expression Profiling

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Ocean Ridge Bioscience's MicroRNA Profiling Service combines high quality microarrays, a reproducible laboratory process, in-depth analysis services, and the best pricing in the industry. ORB's labeling chemistry and hybridization process have been optimized to minimize RNA input requirements. The sensitivity of ORB's microRNA array system enables profiling of microRNA from specimens containing less then 100 nanograms of total RNA including human and rat serum samples, isolated microvesicles, flow-sorted immune cells, and laser-captured microdissected samples. ORB has developed a complete suite of reproducible protocols for isolation, quality assessment, and microarray-based microRNA analysis of RNA from biofluids. The company also has implemented standardized protocols for profiling of microRNA from formalin fixed paraffin embedded (FFPE) tissue. Complementing ORB's laboratory capability for microRNA analysis, the company also provides flexible and comprehensive services for statistical and pathway analysis of microRNA expression data. These capabilities in combination with competitive pricing make ORB a leader in provision of microRNA profiling services and the best solution for effective use of your research funds.

Highlights

  • Reproducible, Sensitive, and Specific
  • Competitive Cost
  • Customized Data Analysis Included
  • Excellent Customer Service

Version 9.0 Multispecies MicroRNA Array

ORB's version 9.0 multispecies microarray provides full coverage of mirBASE version 19, including 2,040 Human, 1,280 Mouse, and 723 Rat mature and minor form(*) microRNAs. The array is triplicate spotted and contains 46 control probes enabling the monitoring of sensitivity, specificity, and reproducibility for every sample hybridized. The array has excellent within experiment reproducibility and also is backward compatible with ORB's previous microarray versions, providing the researcher with the ability to compare current data with previous studies.


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Affymetrix microRNA (miRNA) Microarray

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Ocean Ridge Bioscience's MicroRNA Profiling Service combines high quality microarrays, a reproducible laboratory process, in-depth analysis services, and the best pricing in the industry. ORB's labeling chemistry and hybridization process have been optimized to minimize RNA input requirements. The sensitivity of ORB's microRNA array system enables profiling of microRNA from specimens containing less then 100 nanograms of total RNA including human and rat serum samples, isolated microvesicles, flow-sorted immune cells, and laser-captured microdissected samples. ORB has developed a complete suite of reproducible protocols for isolation, quality assessment, and microarray-based microRNA analysis of RNA from biofluids. The company also has implemented standardized protocols for profiling of microRNA from formalin fixed paraffin embedded (FFPE) tissue. Complementing ORB's laboratory capability for microRNA analysis, the company also provides flexible and comprehensive services for statistical and pathway analysis of microRNA expression data. These capabilities in combination with competitive pricing make ORB a leader in provision of microRNA profiling services and the best solution for effective use of your research funds.

Highlights

  • Reproducible, Sensitive, and Specific
  • Competitive Cost
  • Customized Data Analysis Included
  • Excellent Customer Service

Affymetrix GeneChip miRNA 4.0 Array

Affymetrix GeneChip miRNA 4.0 microarray contains 34,194 probe sets providing complete coverage of mature and pre-microRNA in human, mouse, and rat. The array also contains 1,996 probe sets to cover additional non-coding human small RNA such as snoRNA, CDBox RNA, H/ACA Box RNA, and scaRNA.


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Small RNA Sequencing Data Analysis

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ORB has developed a highly optimized and extensive software pipeline for processing and analysis of small RNA sequencing data backed by extensive research and validation. A wide selection of customizable bioinformatics analysis services are offered to provide our clients with a comprehensive and all-inclusive package to support their data analysis requirements.

Small RNA Analysis Package

  • Full sequencing QC report
  • Sequence read counts and alignment for known microRNAs
  • Fold Changes, 1 and 2 - way ANOVA, T-Tests
  • Principal Component Analysis (PCA)
  • Hierarchical clustering
  • PowerPoint summary
  • Raw FASTQ files

Additional Analysis Options

ORB provides multiple additional custom analysis reports on customer request.

  • Full statistical analysis
  • Alignments for other small RNAs - piRNA, snoRNA, snRNA
  • Sequence read counts, alignment and hierarchical clustering for novel microRNAs
  • MicroRNA target prediction
  • Pathway analysis

Custom Analysis Capabilities

  • Logistic regression
  • Non-parametric testing
  • Mixed-Effect models


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Small RNA Sequencing

Price on request

ORB provides accurate detection and quantification of known and novel microRNAs, piRNAs and several other non-coding RNAs, such as scaRNA, snRNA, snoRNA, and vault RNA; profiling up to 60 million small RNAs per sample by capitalizing on Illumina's new Truseq chemistry and high throughput sequencing technology. ORB can also multiplex small RNA samples on the instrument for a low cost solution and also offers low input service for researchers with minimal amounts of starting material.

ORB uses Illumina's sequencing by synthesis (SBS) technology with TruSeq chemistry for generating unbiased cDNA libraries of small RNA from 1 - 10 ug of total RNA. ORB's standard service offers multiplexed coverage for microRNAs, piRNAs and other non-coding RNAs in the size range of 20-30 bases from 2 ug of total RNA. ORB also offers a proprietary low input protocol for small RNA sequencing from just 30 nanograms of total RNA for researchers working on rare samples such as laser captured cells, flow sorted cells, micro-needle aspirates, micro-dissected tissue and embryonic tissue. Our unparalleled sequencing service package is very competitively priced too!

Highlights

  • Wide coverage of various small RNA categories
  • Illumina's Truseq chemistry or proprietary low input technology
  • Multiplexing for low cost solution
  • Competitively priced complete service package
  • Complete bioinformatics support including statistical analysis

Service package includes:

  • RNA sample quality control and report
  • Library preparation
  • Data QC and Report
  • Complete bioinformatics analysis and report, which includes assembly & alignment to reference, FASTQ files of trimmed sequences, small RNA counting, statistical analysis, and clustering.

ORB can customize the size range for your small RNA discovery project for any small RNA ranging from 20 - 250 bases.

Small RNA Sequencing from Biofluids

ORB has the capability of performing accurate detection, quantification and sequencing of microRNAs from biofluid samples like plasma and serum. This capacity allows ORB to support a wide range of research projects dedicated towards biomarker discovery and RNA profiling.

ORB’s biofluid small RNA sequencing service has direct applications in biomarker discovery as microRNAs are considered to be an ideal class of blood-based biomarkers for cancer detection. Even though the total RNA content in plasma and serum is very low (1-10 ng/ml), the exceptional stability of microRNA in biofluids makes it an important class of biomarker for detection and prognosis of various types of cancers like prostate, lung and colon cancer.

ORB’s ability to isolate circulating microRNAs from biofluid samples like saliva, CSF, lymphatic fluid, and lavage provides researchers from a wide range of scientific backgrounds like cardiology, neuroscience, oncology, reproductive sciences, and molecular diagnostics with the capacity to engage in focused biomarker discovery and development projects.


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RNA-Seq Data Analysis

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ORB has developed a well-documented and tested software pipeline for processing and analysis of mRNA sequencing data on its high-performance computing cluster. A variety of options are offered in order to customize the analysis to meet our client’s experimental objectives.

Standard Analysis Package

  • Full QC report
  • Gene-level sequence read counts
  • Fold changes, 1 and 2-way ANOVA, T-Tests
  • Hierarchical clustering
  • Principal component analysis (PCA)
  • PowerPoint summary
  • FASTQ and BAM files

Additional Options

  • Visualization of sequence reads on the genome scaffold using IGV software
  • Exon-level count (splicing index) statistical analysis
  • Differential splicing and promoter usage using CuffDiff software
  • Pathway Analysis
  • Linear and logistic regression

Specialty Analysis

  • Enhanced alternatively splicing analysis including plotting of exon usage in alternatively spliced mRNAs.
  • De novo transcriptome assembly and blast-based annotation of transcripts from novel species.
  • Correlation of microRNA and mRNA sequencing data.


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RNA Sequencing

Price on request

ORB provides open-platform gene expression profiling on the Illumina HiSeq 2000 and 2500 Sequencing Systems with the sequencing method, coverage, and analysis strategy tailored to fit individual project requirements. Depending on the client application, ORB utilizes library preparation kits from Nugen and Illumina or additional proprietary methods to generate unbiased cDNA libraries with high coverage uniformity. Customers may submit as little as 5 nanograms of RNA, or can benefit from a low cost flat rate service if able to submit a minimum of 2 ug of RNA. ORB backs up its laboratory mRNA sequencing service with full data processing and a complete gene-level data analysis report that is included in our standard service. Alternatively, a wide range of affordable custom data analysis services are available to fit the requirements of nearly any project.

Highlights of ORB's RNA-Seq Service Capabilities

  • Extraction of RNA from a wide variety of tissues and cells including extremely limited source material.
  • Routinely process input RNA amounts of 5-10 nanograms.
  • Flexibility to produce RNA-Seq libraries using a variety of commercial kits available from Nugen, Epicentre, Illumina and others.
  • Low flat-rate pricing for routine mRNA sequencing that is comparable to microarrays.
  • Fully customizable sequencing depth and read length.
  • Advanced bioinformatics capabilities including de novo transcriptome assembly, non-coding RNA analysis, and more.
  • Solid data analysis and presentation capabilities include alternative splicing analysis, linear and logistic regression modeling, and generation of predictive models.

ORB will gladly support your RNA-Seq projects with challenging or unique requirements. Whether its sequencing of immunoprecipitated RNA, sequencing of RNA from subcellular compartments, or ultra-low input situations we welcome the opportunity to work with you! We look forward to hearing from you about your unique project.


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Nucleic Acid Analysis

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Biology

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Sequencing Data Analysis and Management

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Pharmacology & Toxicology

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Biochemistry & Molecular Biology

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RNA Services

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Nucleic Acid Services

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RNA Microarray

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Nucleic Acid Data Analysis

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MicroRNA (miRNA) Microarray

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Biomarkers

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Bioanalysis

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Sheena Knight

M.S., Manager, Technical Communications

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