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New Lab & IT Products for Integrated Biology: Sep 1, 2004



Applied Biosystems SNPbrowser Software Tool

Designed to aid in the selection of SNPs for disease association studies, the SNPbrowser includes data on 20 million genotypes obtained from 160,000 SNPs typed on 180 individuals across four populations. The software also includes a metric linkage disequilibrium map generated from the analysis of the 20 million genotypes that provides information on how to best position SNPs across the genes or regions of interest in a study.

Applied Biosystems


Catalyst 4.9

In the newest release of the drug discovery database management software, Catalyst extends its Linux client and server platform support to include Red Hat 9 and Red Hat Enterprise version WS2.1 and WS3.0. A 2,000-compound trial version of the Catalyst/Jubilant Kinase 2003 database is also now available via Web download. The compounds cover 26 kinase targets and are configured in the database with about 20 property fields.



Ariadne Genomics

Launched in collaboration with Integrated Genomics, Metabolic Vision is a microbial metabolic pathway database compatible with Ariadne’s PathwayAssist software suite. Packages are available for researchers investigating microbial metabolism, including specific packages for bacterial pathogens, antibiotic production, and fungal metabolism. Metabolic Vision combines PathwayAssist’s pathway analysis and visualization tools with Integrated Genomics’ extensive ERGO database of over 600 curated genomes.

Ariadne Genomics


Sun Fire Starter Cluster for Bioinformatics

Built on a V20z Opteron-based server, the latest version of the Sun Fire Starter Cluster for Bioinformatics includes the following upgrades: Redhat Enterprise v3 or Solaris x86 v9; N1 Grid Engine v6; life science applications such as VIBE (Incogen), GenomeQuest (Gene-IT), iNquiry(BioTeam), BioBox (AP Bionet & Sun); a 12-port SMC Tiger 1000 Base-T switch; and a disk that features 2 x 146 GB Ultra320 SCSI drives in Head Node, and a 36 GB Ultra320 SCSI drive in each Compute Node.

Sun Microsystems



Affymetrix GeneChip Mapping 10K 2.0 Array and GeneChip Mapping 100K Array

Both the 10K 2.0 and 100K arrays use the same innovative assay that Affymetrix developed for the earlier GeneChip Mapping 10K Array. Genotyping either 10,000 or 100,000 SNPs requires only one universal primer and a simple protocol.



QIAGEN Pirellula Array-Ready Oligo Set

The new array-ready oligo set contains 7,353 70mer probes representing the complete genetic potential of the marine bacterium Pirellula (Rhodopirellula baltica [Pirellula sp. strain 1]). For probe design, publicly available sequence data from the REGX-Project were used. The Pirellula genome oligo set is provided in a 384-well plate format with 600 pmol of probe per well. A control plate with 24 (12 positive and 12 negative) controls in 16 replicates is also included.



Schott Nexterion Slide MPX

The new Nexterion MPX range of slides allows the simultaneous conduction of multiple microarray experiments on a single slide, ensuring identical experimental conditions. By parallelizing the assay, the new slide also reduces consumption of slides, target material, RNA amplification reagents, and labeling dyes. The slide is comprised of coated glass substrates partitioned into individual wells using a hydrophobic patterning material. Nexterion Slide MPX is available in 16-well and 48-well formats and is offered with all of Schott’s standard coating chemistries.




Stratagene Brilliant Multiplex QPCR Master Mix

The Brilliant multiplex QPCR master mix is designed to amplify three or four targets along with an internal control in the same reaction vessel by using a probe with a different fluorophore for the detection of each amplicon. The Brilliant multiplex QPCR master mix is a convenient 2X formulation of SureStart Taq DNA polymerase, dNTPs, and an optimized multiplex buffer.

(800) 894-1304


USB RT-PCR Master Mix and FideliTaq RT-PCR Master Mix

Designed for one-step RT-PCR reactions in a single tube, the two mixes are available with Taq DNA polymerase for routine detection and FideliTaq DNA polymerase for high-fidelity detection. Targets are easily detected down to 10 pg of total RNA and 100 ng of polyA RNA. By using FideliTaq DNA Polymerase in the mix, amplification fidelity is increased up to six times over Taq DNA Polymerase alone.




Agilent Technologies Multiple Affinity Removal Column

The new multiple affinity removal column removes the three most highly abundant proteins specific to mouse serum. The liquid chromatography column uses immunoaffinity technology to specifically target and remove the three proteins — albumin, immunoglobulin G and transferrin — that comprise approximately 80 percent of the total protein mass in mouse serum. The reusable column can be used for more than 200 experiment runs and can also be used with rat serum.

Agilent Technologies


Applied Biosystems iTRAQ Reagent Kit

The iTRAQ reagent kit contains new, amine-specific, stable isotope reagents that enable relative and absolute quantitation from MS/MS spectra. The reagents expand protein coverage by labeling all peptides including those with post-translational modifications, tag multiple peptides per protein, and have the flexibility to duplex, triplex, or multiplex up to four different biological samples simultaneously in a single experiment.

Applied Biosystems


Ciphergen Biosystems Series 4000 ProteinChip System

The new 4000 series ProteinChip instrument system integrates Ciphergen’s ProteinChip arrays, SELDI-TOF-MS detection, and pattern software in a single system. New features include: novel laser spot rastering, automatic laser energy setting, innovative 104 linear dynamic range detector; a new ion source, flight tube design, and novel detector blanking features which improve ion efficiency and reduce noise; improved system linear dynamic mass range up to 380,000 Daltons; and automated sample handling for unattended runs of up to 168 arrays for large clinical studies.

Ciphergen Biosystems


Target Discovery UltraTrol Pre-coat Reagents for Capillary and Microchannel Electrophoresis

Designed to integrate capillary electrophoresis with mass spectrometry and HPLC systems, the UltraTrol pre-coat reagents help researchers control the direction and magnitude of electro-osmotic force, increasing the resolution, reproducibility, and throughput capabilities of the CE system. The UltraTrol pre-coating reagents are compatible with any capillary or microfluidic electrophoresis systems. They are pH and buffer insensitive, providing selectable and consistent controlled levels and directions of electro-osmotic flow across a wide range of separation conditions. Because the UltraTrol reagents are applied as a pre-coating during CE separations they do not elute with the sample.

Target Discovery



Ambion Drosophila Genome RNAi Library

In collaboration with Cenix BioScience, Ambion is now offering a new RNAi library containing more than 13,000 ready-to-use dsRNAs. The dsRNA designs were created using a proprietary algorithm developed by Cenix that selects optimal gene specific dsRNA sequences with a high degree of accuracy. Cenix has experimentally tested the Drosophila RNAi library in several genome-scale screens using commonly available Drosophila cell lines.




Stratagene GeneMorph II EZClone Domain Mutagenesis Kit

Designed for analyzing the structure-function relationships of proteins and related applications, the GeneMorph II EZClone domain mutagenesis kit features a fast and flexible cloning method for targeted random mutagenesis on individual protein domains. The kit contains Mutazyme II DNA polymerase, which introduces a more uniform mutational spectrum in which mutations at As and Ts occur at the same frequency as Gs and Cs.

(800) 894-1304


Enzo Life Sciences BioArray RNA Amplification and Labeling System

The BioArray RNA amplification and labeling system contains all the reagents for the amplification and biotin labeling of antisense RNA for use with eukaryotic gene expression microarrays. The system includes a cDNA synthesis and in vitro transcription module and a biotin-labeled ribonucleotide mix. In addition, the product makes use of two biotin-labeled nucleotides for maximum incorporation and signal.

Enzo Life Sciences


DNA Research Innovations GeneCatcher DNA Extraction Kits

Designed to handle a wide range of sample volumes, the GeneCatcher Blood Extraction kit is the first in a new range of DNA extraction kits from DNA Research Innovations. The product reliably extracts high levels of pure DNA at a high concentration in a small volume of buffer — even in the presence of anticoagulants — making it ideal for large-scale and high-throughput applications.

DNA Research Innovations
+44 (0) 1795 411 100


QIAGEN EZ1 RNA Universal Tissue Kit

The EZ1 RNA universal tissue kit provides automated purification of total RNA from 1¯6 samples of all types of animal or human tissue. Designed for use with applications such as real-time RT-PCR, arrays, microfluidic assays, and hybridization analysis, the kit integrates efficient phenol/guanidine-based lysis and automated magnetic-particle purification.




Applied Biosystems Expanded TaqMan SNP Genotyping Assays

The newly available assays include an inventory of more than 30,000 TaqMan Coding SNP Genotyping Assays for researchers studying SNPs within protein coding regions of genes, and more than 1.8 million TaqMan pre-designed SNP genotyping assays that can be made to order. The new TaqMan pre-designed SNP Genotyping Assays complement the more than 150,000 validated SNP genotyping assays previously available to provide more robust coverage of the genome for gene-finding, human disease association studies, and other applications.

Applied Biosystems


To tell GT about new recently released products, e-mail John MacNeil, Senior Editor, at [email protected]

The Scan

Unique Germline Variants Found Among Black Prostate Cancer Patients

Through an exome sequencing study appearing in JCO Precision Oncology, researchers have found unique pathogenic or likely pathogenic variants within a cohort of Black prostate cancer patients.

Analysis of Endogenous Parvoviral Elements Found Within Animal Genomes

Researchers at PLOS Biology have examined the coevolution of endogenous parvoviral elements and animal genomes to gain insight into using the viruses as gene therapy vectors.

Saliva Testing Can Reveal Mosaic CNVs Important in Intellectual Disability

An Australian team has compared the yield of chromosomal microarray testing of both blood and saliva samples for syndromic intellectual disability in the European Journal of Human Genetics.

Octopus Brain Complexity Linked to MicroRNA Expansions

Investigators saw microRNA gene expansions coinciding with complex brains when they analyzed certain cephalopod transcriptomes, as they report in Science Advances.