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.Read More
The BiosearchTech Blog
Topics: RNA FISH
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.Read More
Topics: RNA FISH
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.Read More
Topics: RNA FISH
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:
- 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.
- 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.
- 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.
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?
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.
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.
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.
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.
Topics: RNA FISH
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.