The BiosearchTech Blog

Shining a light on gene expression and regulation one cell at a time

Posted on Thu, Apr 19, 2018 @ 10:51 AM

To truly understand complex diseases such as cancer, scientists need access to tools that don’t just average data across millions of cells, but that can interrogate single cells to examine  gene expression and regulation in diseased cells. 

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Topics: RNA FISH, Genomics, Stellaris

A Stellar-is Year in the Making

Posted on Wed, Dec 07, 2016 @ 08:05 AM

 It wouldn't be fair to close out 2016 without showcasing the stellar year that Stellaris® RNA FISH has had. Take a closer look at our top 10 highlights from the past year - mind blowing images are only the beginning!

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Topics: Product Information, RNA FISH, Genomics, Stellaris

Imaging Stellaris Assays Part III: Creating Professional, Publication-ready Images

Posted on Thu, Mar 10, 2016 @ 02:00 PM

Here is the final installment of our “Imaging Stellaris Assays” blog series. In our two previous posts, we’ve gone over microscope hardware and image acquisition.  In this article, we will walk you through some simple downstream image processing that will turn your raw Z-stack images into spectacular-looking, publication-ready images.

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Topics: RNA FISH

Welcome to the Stellaris® Citation Center

Posted on Thu, Feb 11, 2016 @ 02:16 PM


We have recently released a Stellaris® RNA FISH Citation Center to make it easy to find publications related to your areas of interest. Incredibly, a full third of these hundreds of papers are published in Nature, Science, or Cell, indicating both the tremendously high quality of our customer’s work as well as the potential value of including Stellaris RNA FISH in your publications. The number of citing publications is growing precipitously each year and now includes a wealth of protocols, references, and technologies including super-resolution and STORM microscopy, whole mount, targets including viruses and plants, CLARITY, and other cutting edge applications. The citation center is updated several times a month to ensure that the most recent publications are always available.

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Topics: RNA FISH

Designing Stellaris RNA FISH Probes Part I: Increasing Probe Count

Posted on Thu, Jan 14, 2016 @ 02:00 PM

Stellaris® RNA FISH is a novel technology that allows for the detection of single or clustered RNAs in fixed cells and tissue. Multiple unique probes with similar stability are designed to hybridize along the length of a single RNA target and upon hybridization, generate a fluorescent signal. LGC Biosearch Technologies offers customers a web-based, free, and easy to use software for Stellaris RNA FISH Probe design. The probe designer takes an input sequence, such as an mRNA coding sequence, and outputs a set of up to 48 probes designed for optimal binding properties.

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Topics: RNA FISH

Imaging Stellaris Assays Part II: How to Acquire Stunning Images

Posted on Thu, Sep 24, 2015 @ 02:30 PM

Here we continue our “Imaging Stellaris Assays” blog series.  We last left off talking about the most important components: the microscope and the hardware features necessary to detect your Stellaris signal. In this blog article, we will walk you through the technique of finding your cells and acquiring a sharp and stunning image. 

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Topics: RNA FISH

Runaway RNA Stays Put

Posted on Thu, Sep 17, 2015 @ 02:00 PM

The cleavage and polyadenylation event, the final trimming in the molecular mRNA barbershop, normally releases both the finished styled mRNA, and the stylist. But, in salt-stressed cells, as there are fewer transcription starts, the polymerase stays busy, and keeps on going, and going, down the template strand as if there were no end in sight. Then, as the cell has finished acclimatizing to the new environment, and as promoter-guided gene transcription starts up again, the previously unwanted RNA growth can now serve as a guide for the barber to find a chair with a new customer in need of styling. RNA-style. Cap first, then splice, and lastly, trim the ends.

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Topics: RNA FISH

Imaging Stellaris Assays Part I: Get to Know Your Microscope

Posted on Thu, Aug 27, 2015 @ 05:00 PM

Stellaris® FISH is an RNA detection technology performed by means of in situ hybridization. This technology and all of the incredible applications it supports would not exist without a detection tool. The detector in this scenario is a fluorescence microscope. 

The microscope is the single major limitation for scientists who are new to the Stellaris technology. The reason being – well, this is a new technology and fluorescence microscopes are not ordinary instruments found in every lab across the country. These are highly intricate, sensitive, and costly pieces of real estate that reside primarily in core laboratories to provide additional interrogation of biological systems through optics. With that said, every microscope system is unique. In other words, it’s not a packaged deal, but rather entirely customized. From the nuts and bolts of the hardware to the software that coordinates all your movements, every piece is different from one lab to the next. Streamlining a protocol for each and every combination of system imaginable would be impractical. So whether your lab uses Nikon, Leica, Olympus, Zeiss, or something else, this blog article is intended to share fundamental microscope requirements to help you obtain a great Stellaris image.

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Topics: RNA FISH

And the Consensus (Sequence) is...

Posted on Thu, Jun 11, 2015 @ 02:31 PM

Studying the expression level of RNA transcripts is often complicated by the fact that many DNA sequences are transcribed into multiple RNA isoforms. Or, in cases with microbes, each strain can represent a different sequence variant due to the frequency of mutations in these organisms. Despite these complications, it is still possible (in some, but not all, cases) to design a functional assay to detect multiple variants or isoforms of a gene or transcript. In other words, design one assay to specifically detect multiple targets. In this article, we will go over the basics of designing your assay to detect multiple transcripts at once.

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Topics: Real-time PCR, RNA FISH

Research Highlight: Bringing Vision Research into Focus

Posted on Thu, May 28, 2015 @ 02:14 PM

Gene expression and molecular biology research in vision and ophthalmology presents unique challenges to researchers and clinicians due to the complexity of the eye. The eye consists of many structures containing specific cell populations, each exhibiting different expression profiles. Such an intricate organ requires a series of advanced methods in your molecular toolkit to unlock the mechanisms of degenerative eye disease.

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Topics: RNA FISH

FISH-ing for Fusions: A unique approach to fusion gene mRNA & pre-mRNA detection in cancer

Posted on Fri, May 15, 2015 @ 01:00 PM

This past April, Biosearch attended the American Association of Cancer Research (AACR) conference in Philadelphia, PA where, in collaboration with Byung Chul Kim from Clinomics, Inc, we shed light on the detection of fusion genes by means of Stellaris® RNA FISH. Gene fusions have the potential to activate otherwise silent signaling enzymes, such as the anaplastic lymphoma receptor tyrosine kinase (ALK), leading to significant numbers of lung and other related cancers. This particular gene fusion occurs from inversions on chromosome 2 (inv2(p21p23)), fusing the EML4 and ALK genes and connecting the promoter and 5' half of EML4 (active in normal lung tissue) together with the 3' and kinase encoding half of the otherwise silent ALK gene.

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Topics: RNA FISH

Research Highlight: Localizing long non-coding RNA (lncRNA)

Posted on Thu, Mar 12, 2015 @ 02:00 PM

A recent paper published in Molecular Cell by Dimitrova et al. from the lab of Dr. Tyler Jacks at MIT, used Stellaris® RNA FISH to help answer questions regarding whether a pro-apoptotic lncRNA (lncRNA-p21) can regulate nearby genes via cis- or trans-acting mechanisms1. Long non-coding RNA-p21 and p21 expression is stimulated in response to the activation of the p53 pathway. This pathway is an important area of study because it is involved in tumor suppression and is elicited in response to DNA damage and cellular stress.

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Topics: RNA FISH

The 4Cs of Stellaris® RNA FISH Buffers

Posted on Thu, Feb 26, 2015 @ 02:00 PM

Buffers are often overlooked and taken for granted until the day comes when a peculiar result is observed and its origin is traced to a bad buffer. Although in very rare cases mistakes in the composition of buffers have led to discoveries such as the correct number of human chromosomes1, using properly prepared buffers can be the key to success with technologies such as Stellaris RNA FISH.

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Topics: RNA FISH

Unraveling the Neural Web: Stellaris® RNA FISH for Neuroscience Research

Posted on Thu, Nov 13, 2014 @ 03:45 PM

Neuroscience gene expression research can come with many hurdles, especially when working with brain tissue or mixed populations of cultured neurons. Here are just a few obstacles Neuroscientists run into:

  1. The brain is not made only of neurons! Alongside neurons, brain tissue can contain a variety of cell types such as glial cells and oligodendrocytes.These cell types may act separately or in conjunction with each other to perform a specific function.
  2. The brain itself is regionally heterogeneous, containing specialized anatomical structures such as the amygdala, hypothalamus, and hippocampus. These regions perform distinct functions such as eliciting the fight or flight response, signaling reproduction, or contributing to memory.
  3. Even so, delving within each of these brain regions, you will find even more specialization. Certain cell populations express a particular RNA signature. For example, tyrosine hydroxylase (Th) expression in dopaminergic neurons, which is critical to the synthesis of the neurotransmitter dopamine. Cells surrounding Th cells, or interspersed with Th cells do not express Th at all! These are all contributing factors that make neuroscience so incredibly fascinating, yet so cumbersome.
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Topics: RNA FISH, Lab Method

Five Ways Controls Can Demystify Your Stellaris® RNA FISH Experiment

Posted on Tue, Nov 04, 2014 @ 02:13 PM

Stellaris controls, who needs ‘em? We all do. Especially if it’s your first time interrogating a sample with a new Stellaris RNA FISH probe set, it is critical to consider the proper controls. The concept of positive and negative controls for experiments is not a new one. Far too often, we tend to bypass the consideration of controls in favor of saving time. However, it really all boils down to, “how do you, as a scientist, interpret your results after the experiment is over?”

Positive and negative controls for Stellaris experiments can be viewed from multiple angles. Let’s say you were successful in measuring spots on your first try, the major questions you may ask are:

  • Is the signal I am measuring being produced by probe bound to RNA?
  • Are these spots true signal or just background?
  • Are these spots specific to my target or are they picking up other RNAs?
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Topics: RNA FISH, Lab Method

Biosearch Technologies Executes Exclusive License for turboFISH™

Posted on Mon, Oct 07, 2013 @ 07:29 AM

Biosearch Technologies, Inc. (Biosearch), a leading supplier of sophisticated oligonucleotide components to the rapidly growing molecular diagnostics industry announced today that it has acquired exclusive worldwide rights to turboFISH technology - A Method for Rapid Single Molecule RNA FISH. With this turboFISH license, Biosearch maintains exclusive access to continuing Stellaris® RNA FISH based inventions from Rutgers, The State University of New Jersey.

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Topics: Announcement, RNA FISH

Biosearch Technologies Acquires Majority Stake in LightSpeed Genomics

Posted on Wed, Sep 25, 2013 @ 07:25 AM

Biosearch has acquired a majority stake in LightSpeed Genomics, Inc. (LSG), a Santa Clara, California-based company developing an innovative optical detection solution for the life science and diagnostics industry based on its proprietary Synthetic Aperture Optics™ (SAO™) technology. Biosearch and LSG are collaborators on the development of StellarVision™, a next generation gene expression platform optimized to work seamlessly with Biosearch’s Stellaris® RNA FISH assays to detect and quantify single molecule RNA targets within individual cells.

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Topics: Announcement, RNA FISH

RT-qPCR and the Stellaris FISH Method

Posted on Fri, Apr 26, 2013 @ 10:32 AM

A "Referral from the Doctor" Blog Article-

Quantitative reverse transcription polymerase chain reaction (RT-qPCR) is a sensitive and
robust method for analyzing RNA. It has been used to corroborate the findings of other genetic methods, such as microarray and RNAse protection assays, and has become the gold standard for quantifying changes in gene expression. Stellaris FISH is a new RNA detection method that provides direct quantification of transcripts in situ, with potential to become the standard for mRNA and lncRNA interrogation using microscopy.

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Topics: Real-time PCR, RNA FISH, Referral from the Doctor

Stellaris® Foundation Genes: GAPDH

Posted on Thu, Apr 11, 2013 @ 09:30 AM

Stellaris probe sets targeting glyceraldehyde-3-phosphate dehydrogenase (GAPDH) mRNA were among the first designed at Biosearch Technologies. Due to the long history of its use as a control in northern blots and real time qPCR, GAPDH was a natural choice for an initial housekeeping gene. The use of probes targeting GAPDH in Stellaris assays, however, is somewhat more nuanced. GAPDH is highly expressed in most all cell types – in our tests of the probe set in A549 cells, we counted upwards of 2000 copies per cell. With such high expression, the GAPDH probe set is ideal for testing filter set and microscope compatibility, as well as assay preparation. Positive signal is immediately obvious due to the high number of transcripts per cell.

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Topics: RNA FISH

Biosearch Technologies, UMDNJ Stellaris® Probe Alliance - NextGen Gene Expression™, SNP FISH™, and iceFISH™ in Research and Clinical Applications

Posted on Mon, Mar 18, 2013 @ 08:43 AM

Biosearch Technologies, Inc. (Biosearch), a leading supplier of sophisticated oligonucleotide components to the rapidly growing molecular diagnostics industry, today announced that the company has acquired exclusive worldwide rights to continuing Stellaris® RNA FISH based inventions from the University of Medicine and Dentistry of New Jersey (UMDNJ).  In addition to single molecule detection of mRNA, lncRNA, and viral RNAs, Stellaris based methods have been extended to directly and quantitatively detect chromosomal diseases caused by translocations and aberrant splice junctions,(intron chromosomal expression – iceFISH™) and single-nucleotide polymorphisms (SNPs or SNP FISH™).  Biosearch’s exclusive access to Stellaris probe design is offered complimentary at www.biosearchtech.com/stellarisdesigner.

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Topics: Announcement, RNA FISH

Biosearch Technologies Launches Catalogued Stellaris™ RNA FISH Assays

Posted on Mon, Jun 18, 2012 @ 08:08 AM

Biosearch Technologies, Inc. (Biosearch), a leading supplier of sophisticated oligonucleotide components to the rapidly growing molecular diagnostics industry, today announced that the company has launched catalogued assays for Stellaris™ RNA FISH. These assays fall into three groups – well characterized RNA targets (“foundation genes”) suitable for use as positive controls, oncogenes, and key mRNAs in the hypusine pathway.

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Topics: Announcement, RNA FISH

Single molecule viral RNA analysis using Stellaris™ FISH technology

Posted on Wed, May 30, 2012 @ 01:00 PM

  Image courtesy of: http://www.cdc.gov/h1n1flu/images.htm

A cooperative effort between researchers at Mount Sinai School of Medicine in New York and the University of Illinois at Urbana-Champaign demonstrates a novel experimental system for single-molecule sensitivity FISH analysis of individual virus particles. 

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Topics: Biodefense, RNA FISH

Biosearch Technologies Launches Improved RNA FISH Design Software

Posted on Mon, Mar 19, 2012 @ 07:54 AM

Biosearch Technologies, Inc. (Biosearch), a leading supplier of sophisticated oligonucleotide components to the rapidly growing molecular diagnostics industry, today announced that the company has launched an improved Stellaris™ Probe Designer. The online, RNA FISH design software provides scientists with a means to design Stellaris RNA FISH probe sets against any mRNA or long noncoding RNA.

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Topics: Announcement, RNA FISH

Stellaris FISH Workshop at the AMP 2011

Posted on Tue, Nov 15, 2011 @ 01:53 PM

Join us at AMP 2011 on November 16th for a live demonstration of the Stellaris technology at the Gaylord Texan Resort in Grapevine, TX. Biosearch Technologies’ lead Stellaris research scientist, Arturo Orjalo, PhD will demonstrate the preparation and fluorescent imaging of single molecule messenger RNA in fixed cells. The workshop will take place in the Texas 1 room at 1:00PM.

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Topics: RNA FISH, Lab Method

Blogging about Stellaris™ RNA FISH at Singlemoleculefish.com

Posted on Mon, Oct 24, 2011 @ 12:24 PM

Biosearch Technologies is starting a new sister blog at singlemoleculefish.com where all articles will focus on topics related to Stellaris RNA FISH. We will be doing our best to provide as many resources as possible to help you understand the potential of this new RNA FISH technology.  You can keep up with the latest by attending AMP's 2011 Annual Meeting at Grapevine, TX. At this molecular pathology conference, Biosearch will be conducting a Stellaris FISH workshop on Weds, November 16 at 1PM in room Grapevine 2.

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Topics: Announcement, RNA FISH

Biosearch Technologies Announces Release of Custom Stellaris™ FISH Probes

Posted on Mon, Sep 12, 2011 @ 04:59 AM

Stellaris FISH advances research in cancer, developmental biology and pathology by resolving in situ messenger RNA into clear focus.

Biosearch Technologies, Inc. (Biosearch), a leading supplier of sophisticated oligonucleotide components to the rapidly growing molecular diagnostics industry, today announced the release of an empowering new product, Stellaris FISH Probes*. Stellaris FISH (fluorescence in situ hybridization) is a RNA visualization method that allows simultaneous detection, localization, and quantification of individual mRNA molecules at the sub-cellular level in fixed samples.

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Topics: RNA FISH

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About LGC, Biosearch Technologies

LGC, Biosearch Technologies is the complete Genomics portfolio from LGC. Providing genomic analysis tools, instrumentation and services to the genomic scientific discovery sector worldwide, with focus on across ag bio, pharma and molecular diagnostics. Visit our home page to view our products and services.

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