Mar

18

Transcriptome Analysis

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by Jeffrey M. Perkel

Once the domain of microarrays – the previous decade’s hot technology — transcriptome analysis (that is, gene expression monitoring on a genome-wide scale) is now associated with the current “it” technology: Next-generation DNA sequencing.

Though such data can be collected using arrays (sequencing was previously used mostly for transcript discovery), with sequencing “You are not limited to what you probe,” he explains. “You can discover new things.” In other words, sequencing approaches, unlike microarrays, are unbiased – “hypothesis-neutral,” in Baker’s words – meaning you can find things you weren’t looking for, and reanalyze the data later as new discoveries come to light…

[Gene-expression microarrays still hold some advantages over sequencing.]

…Not everyone has access to a next-gen DNA sequencer for one thing, and even if they do, they may not be able to get instrument time when they need it.

More critically, sequencing is generally time-consuming (one to two weeks per run, typically), expensive, and bioinformatically challenging – all of which presents a problem for independent researchers outside of major sequencing centers, and especially, for diagnostics developers.  (read more)

Jan

20

Seminar – MicroRNA Discovery & Profiling

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Presented by – Dr. Christoph Eicken & Dr. Qi Zhu, LC Sciences
12:00 pm Conference Room 2

as part of – Texas Medical Center BioResearch Product Faire

Houston, TX (Marriott Medical Center) – January 16, 2010

Nov

13

Custom MicroRNA Microarray – a Tool for Plant Research

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coconut_chips_blog

Many recent studies report that miRNAs control the key components of signaling pathways and thereby regulate related development processes in plants.  LC Sciences offers several options for study of plant microRNA.  In addition to our standard microarrays designed for all plants in the miRBase 14.0 (1,117 unique miRs) and the Plant MicroRNA Database 1.0 (5,690 unique miRs), our custom microfluidic platform enables the synthesis of made to order custom plant microarrays.

Researchers at the Laboratory of Tropic Biological Resources, Hainan University, China utilized a custom plant microRNA microarray from LC Sciences to study cellular development in coconut, a key plantation crop in the tropical parts of the world1. The custom µparaflo® microfluidic chip contained 653 unique plant miRNAs of release version 10.1 (http://www.mirbase.org/), representing 877 miRNAs from 17 plant species. The 877 miRNAs comprised 154 from Arabidopsis thaliana, 115 from Oryza sativa, 187 from Physcomitrella patens, 100 from Populus trichocarpa, 43 from Zea mays and 278 from 12 other plant species.

Comparative analyses of the miRNA expression profiles between developmental stages of coconut endosperm showed that several miRNAs were differentially expressed in mature tissue. Differential expression was confirmed using real-time PCR. The contrasting expression patterns between the two developmental stages suggested that miRNAs play a role in tissue development and compound metabolism of coconut endosperm.

Li D, Zheng Y, Wan L, Zhu X, Wang Z. (2009) Differentially expressed microRNAs during solid endosperm development in coconut (Cocos nucifera L.). Scientia Horticulture 122(4), 666-69. [abstract]

Sep

22

Featured Publication

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An essential role of microRNAs in reactive oxygen species-mediat Researchers at the RNA and Cardiovascular Research Laboratory, New Jersey Medical School have studied microRNA in acute myocardial infarction by expression profiling of miRNA in rat hearts with microarray. Their results suggest that miRNAs may play important roles in the phathophysiology of AMI. Some miRNAs may be considered new therapeutic targets or even biomarkers for ischemic heart disease such as AMI. [abstract]

Sep

21

microRNA Microarray Service

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LC Sciences provides a genome-wide microRNA (miRNA) expression profiling service using µParaflo®technology and proprietary probe design, which enable highly sensitive and specific direct detection of miRNAs. We have standard arrays for mature miRNA of all species available in the latest version of the miRBase database (Release 14.0). Our service is comprehensive and includes small RNA enrichment from your total RNA sample, single or dual color labeling, hybridization, image data processing and in-depth data analysis. Two-three weeks after receiving your total RNA samples, we send you the analyzed data, representative and original images of the array, and raw data. We offer additional products and services including arrays containing miRNA*, walk/tiling arrays, custom arrays (first 100 probes free of charge), and in-depth analysis for multiple data sets. The in-depth data analysis may include multi-array normalization, t-test, ANOVA, False Discovery Rate calculator, and/or clustering analysis.

Sep

17

Featured Publication

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Yale researchers put LC Sciences’ microRNA Microarray Service to work to study microRNA involvement in obesity.  Their results strongly suggest that miR-27 represents a new class of adipogenic inhibitors and may play a role in the pathological development of obesity.  [abstract]