Technical Article

General Considerations The time to start thinking about validating your microarray results is not after you have completed your experiment, but instead before you start. Generally, your ability to validate results is dependent on the statistical validity of your data which is in turn dependent on good experimental design. Good experimental design is essential to ensure statistically significant results and to justify scientific conclusions. Good basic experimental design includes randomization of

The gestational state is a period of particular vulnerability to diseases that affect maternal and fetal health. Stress during gestation may represent a powerful influence on maternal mental health and offspring brain plasticity and development. In a fascinating new study,  a team led by researchers at the University of Lethbridge, Canada show that the fetal transcriptome, through microRNA (miRNA) regulation, responds to prenatal stress in association with epigenetic signatures of psychiatric and

MicroRNAs (miRNAs) are endogenous regulators of a broad range of physiological processes and act by either degrading mRNA or blocking its translation. Mature miRNAs function within large complexes to negatively regulate specific target mRNAs. Plant miRNAs generally interact with their targets through perfect or near-perfect complementarity and direct mRNA target degradation. In plants, miRNAs not only post-transcriptionally regulate their own targets but also interact with each other in regulatory networks to affect many aspects of development, such as growth, development and

A team led by researchers at the Keio University School of Medicine, Tokyo used a miRNA microarray performed by LC Sciences to investigate the molecular pathogenesis of gastric mucosa-associated lymphoid tissue (MALT) lymphoma1. Analysis of the miRNA expression profile in tissue specimens from gastric MALT lymphomas and surrounding non-tumor mucosae revealed that a hematopoietic-specific miRNA miR-142 and an oncogenic miRNA miR-155 were overexpressed in MALT lymphoma lesions. The expression levels of

MicroRNAs (miRNAs) are endogenous regulators of a broad range of physiological processes and act by either degrading mRNA or blocking its translation. Mature miRNAs function within large complexes to negatively regulate specific target mRNAs. Plant miRNAs generally interact with their targets through perfect or near-perfect complementarity and direct mRNA target degradation. In plants, miRNAs not only post-transcriptionally regulate their own targets but also interact with each other in regulatory networks to affect many aspects of development, such as growth, development and

MicroRNAs (miRNAs) are endogenous regulators of a broad range of physiological processes and act by either degrading mRNA or blocking its translation. Mature miRNAs function within large complexes to negatively regulate specific target mRNAs. Plant miRNAs generally interact with their targets through perfect or near-perfect complementarity and direct mRNA target degradation. In plants, miRNAs not only post-transcriptionally regulate their own targets but also interact with each other in regulatory networks to affect many aspects of development, such as growth,

An Excerpt From “In the fast lane: Large-scale bacterial genome engineering” Traditional applications of short, synthetic oligos in recombinant DNA technology include the introduction of restriction enzyme recognition sites for cloning, mutagenesis of a DNA segment, priming of PCR amplifications, and pasting together recombinant molecules. Today, the large scale and relatively low cost of short oligo synthesis with new oligo assembly techniques has resulted in replacing classic construct engineering by DNA synthesis, now frequently outsourced to commercial providers. Most DNA

MicroRNAs (miRNAs) represent a family of small noncoding RNAs controlling translation and transcription of many genes. As post-transcriptional gene regulators, they are involved in various fundamental biological processes as well as in diseases. The cellular response to virus infection is initiated by recognition of the invading pathogen and subsequent changes in gene expression mediated by both transcriptional and translational mechanisms. Although the viral receptor is an important factor

Molecular Diagnostics / Biomarkers – Identification of specific miRNAs or miRNA expression based signatures that can act as biomarkers for various diseases/pathologies. Make accurate and detailed clinical diagnosis Determine prognosis and predict treatment efficacy Monitor and assess the health effects of environmental and other toxicants Drug Discovery / Therapeutics – Identification of miRNAs that play essential roles in disease to act as drugs or possible therapeutic targets

Archiving histological tissue samples by formalin-fixing and embedding in paraffin blocks (FFPE) has been a routine practice for medical and research institutions for many years. These samples are very valuable because they are well annotated with rich patient data and medical history. It has been demonstrated in multiple studies that miRNA is minimally affected by FFPE treatment and microRNA extracted from FFPE samples provides reliable expression levels.  (read the entire application note…)  White

Recent major advances in DNA sequencing technologies have resulted in several new “next-generation” platforms capable of generating massive amounts of reads very quickly and relatively inexpensively.  These new technologies hold the promise of one day, routinely sequencing entire complex eukaryotic genomes. Next-generation DNA sequencing (NGS) has broad applications in both research and clinical diagnostics and has specifically become an important platform for identifying mutations and variants from clinical samples.

New technical bulletins are now available online for our microRNA Microarray Service. Technical Bulletin - Experimental Design for Microarray Experiments Technical Bulletin - Probe Content Selection Technical Bulletin - RNA Sample Quality Control

Over the last two decades, the introduction of microarray technology has had a profound impact on gene expression research. However, early on there was some definite variability in the reported results1, as can be expected with new technologies, and as we are now seeing with RNA-Seq gene expression results2. The publication of studies with variable or contradictory results, obtained using different microarray platforms to analyze identical RNA samples, had raised concerns about the reliability of this technology. It follows that

Modern synthetic biology involves not only the construction of existing genes to elicit their functions, but also designed mutation and sequence shuffling to create new, functional gene constructs to perform as biomolecular machines. The ability to mass produce these synthetic constructs and perform simultaneous assembly will have a significant impact on research in biology and medicine. Multiplex, parallel DNA construction on a large scale requires pools of large numbers of short synthetic oligonucleotides (oligos).

Recently, some creative thinking scientists have put microarrays, and more specifically, oligonucleotides synthesized on microarrays, to use in a host of applications1. LC Sciences offers our OligoMix® product for use in these and other applications.  You can find out more about OligoMix® here. Microarray synthesized oligos are being used for these and other applications: Synthesize  massive scale RNA interference libraries. Create libraries of thousands to millions of oligonucleotide probes, each

Microarray-based analysis of cadmium-responsive microRNAs in rice (Oryza sativa). MicroRNAs (miRNAs) are a class of small non-coding RNAs that negatively regulate specific target mRNAs at the post-transcriptional level. Plant miRNAs have been implicated in developmental processes and adaptations to environmental stresses. Cadmium (Cd) is a non-essential heavy metal that is highly toxic to plants. To investigate the responsive functions of miRNAs under Cd stress, miRNA expression in Cd-stressed

To meet the growing demand for synthetic genes, more robust, scalable and inexpensive gene assembly technologies must be developed. Methods for large-scale, high-quality gene synthesis at an affordable price are needed for advances in both synthetic biology and biotechnology. One limitation for gene synthesis is the cost of making the building blocks (oligonucleotides) that are assembled together to make genes. Current oligonucleotide synthesis methods via standard solid support synthesis cost ~ $0.20/bp.

MicroRNAs (miRNAs) are small non-coding RNAs found in eukaryotic organisms that regulate gene expression. Dismissed as “junk” until about a decade ago, it is now widely accepted that they play an important functional role in a wide array of cellular processes. MiRNAs regulate gene expression by targeting individual or multiple messenger RNAs (mRNAs). Perfect or partial base pairing with the target mRNA promotes cleavage of the RNA in plants

PIWI proteins are bound to a novel class of germ cell specific small RNAs called Piwi-interacting RNAs (piRNAs).  Piwi proteins and their partner small RNAs play an essential role in fertility, germ-line stem cell development, and the basic control and evolution of animal genomes. Differential expression analysis of piRNA by custom microarray was used in part to gain a better understanding of piRNA biogenesis1. Comprehensive analysis by custom microarray of piRNA expression in fetal male germ cells deficient in various PIWI family

The development of next generation technologies is enabling the complete mapping and further understanding of microRNAs (miRNAs).  Deep sequencing (NGS) provides complete coverage of the small transcriptome and new bioinformatics tools such as ACGT101-miR enable an exhaustive analysis of the sequencing data. The application of these new technologies together with the availability of a nearly complete pig genome has provided the basis for further defining the molecular and cellular function of these small regulatory molecules in the pig. The domestic pig