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

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BIOINFORMATICS

Ingenuity Pathway Analysis Application (updated)

The updated Winter 2004 version of Ingenuity’s Pathway Analysis Application cross- references its networks with canonical metabolic and signaling pathways, is optimized for networks of up to 35 nodes, supports Swiss-Prot identifiers for proteomic data analysis, and supports two new Affymetrix GeneChip microarrays, HG-U133 Plus 2.0 and HG-133A 2.0.

Ingenuity

650.967.7777

www.ingenuity.com

Lion Bioscience SRS Gateway for Oracle

The new module of the SRS architecture allows bioinformaticists to access the SRS engine and associated databases from Oracle using SQL. The SRS Gateway for Oracle is available immediately for SRS 7.1 and supports Oracle9i Database Release 2 and subsequent versions including Oracle Database 10g.

Lion Bioscience

617.245.5400

www.lionbioscience.com

Tecan Freedom EVOware Software

Designed to control Tecan’s Freedom EVO robotic liquid handling system, Freedom Evoware also provides pipetting and dynamic scheduling of multiple devices.

Tecan

800.832.2687

www.tecan.com

BIOLOGICAL ASSAYS

Panomics SH2 Domain Array

Panomics'''''''' TranSignal SH2 Domain Array is a tool for identifying interactions between tyrosine-phosphorylated ligands and 34 types of SH2 domains that remain folded in active conformations.

Panomics

877.726.6642

www.panomics.com

Promega ProFluor Tyrosine Phosphatase Assay

The ProFluor tyrosine phosphatase assay measures purified tyrosine phosphatase activity in a multiwell plate format. Tyrosine phosphatases tested with the assay include PTP-1B, CD45, LAR PTPase, T-cell PTPase and YOP-51.

Promega

800.356.9526

www.promega.com

Qiagen LiquiChip bead-based xMAP assay kits

Two new LiquiChip bead-based xMAP assay kits from Qiagen are designed to detect a wide range of Tyr and Ser/Thr kinase activities without the need for radioactivity. The effect of potential or known inhibitors on kinases can also be investigated.

Qiagen

800.426.8157

www.qiagen.com

Stratagene Vitality hrGFP II Mammalian Expression Vectors

The Vitality hrGFP II fluoresces brighter and is less toxic than EGFP, according to Stratagene. HrGFP II is optimized for mammalian expression studies, and is detectable by fluorescence microscopy and flow cytometry.

Stratagene

800.424.5444

www.stratagene.com

IMAGING

PerkinElmer Lambda series UV/Vis/NIR Spectroscopy Instruments

The upgraded Lambda series of instruments for ultraviolet, visible, and near-infrared spectroscopy from PerkinElmer includes a new Universal Reflectance Accessory, which automates angle changes, eliminates alignment issues, and permits instant switching between reference and sample.

PerkinElmer

866.250.6070

www.perkinelmer.com/lambda

Tecan Safire 2 Monochromator-based Microplate Reader

Allowing high-throughput screening and assay development to be performed on one instrument, the Safire2 provides detection modules for top and bottom fluorescence intensity measurements, fluorescence polarization studies, and multi-channel absorbance and luminescence measurements.

Tecan

800.832.2687

www.tecan.com

LIMS

LabVantage Sapphire version 3.2 LIMS software

LabVantage’s Sapphire version 3.2 LIMS software now includes support for Oracle 9i, enhanced Java API supporting SDK V1.4.2_02, new Workflow Actions to support Crystal Enterprise Professional Edition Version 9, and Sapphire Console, a wizard-based installation and upgrade function.

LabVantage

888.346.5467

www.labvantage.com

Liquid Handling

Tecan Cavro XLP 6000

Introduced in the US for the first time, the Cavro XLP 6000 is a high-performance syringe pump with 6,000 (standard 6,000/48,000) increment resolution.

Tecan

800.832.2687

www.tecan.com

MICROARRAY ANALYSIS

Illumina Sentrix Whole-Genome BeadChips

Illumina’s first new BeadChip is designed to analyze six discrete whole-human-genome samples on one chip, interrogating in each sample approximately 48,000 transcripts from the estimated 30,000 genes in the human genome. The second BeadChip product analyzes eight samples in parallel against the roughly 22,000 genes represented in the consensus RefSeq database.

Illumina

800.809.4566

www.illumina.com

Nunc ArrayCote Microarray Slides and Plates

Nunc offers a lidded, removable 16-well chamber microscope slide for microarray experiments. The slides are coated with aminopropylsilane, epoxy, or aldehyde, and are compatible with standard microarray scanners. Nunc also offers the ArrayCote in a 96-well plate format.

Nunc

866.688.2548

www.nuncbrand.com

Qiagen Grape Array-Ready Oligo Set

The new grape (Vitis vinifera) array-ready oligo set contains 14,562 probes of 70-mers representing grape gene transcripts. Probe design for the grape oligo set is based on sequence information from TIGR’s Grape Gene Index (VvGI) release 3.

Qiagen

800.426.8157

www.qiagen.com

Schleicher & Schuell BioScience FAST Quant TH1/TH2 Antibody Microarrays

Designed for scientists assaying multiple cytokines, Schleicher & Schuell’s FAST Quant TH1/TH2 quantitative antibody microarrays provide quantitative detection of nine cytokines in each of 56 samples on standard nitrocellulose coated glass slides, using a microplate footprint.

Schleicher & Schuell

800.245.4024

www.schleicher-schuell.com

VizX Labs GeneSifter.Net Version 2004.1 Microarray Analysis Software

The most recent version of GeneSifter.Net includes features specific to Affymetrix microarray users, including the Robust Multi-array Average (RMA) probe-level analysis method, a unique Gene Ontology report using z-score statistics to target particular families of genes, MIAME-compliant protocols, and statistical analysis techniques.

VizX Labs

877.932.4363

www.genesifter.net

PCR

Becton Dickinson qPCR Human Reference Total RNA

Designed as a reference standard for quanitative RT-PCR experiments, BD’s qPCR Human Reference Total RNA is pooled from whole human tissues to offer broad gene coverage. The reference RNA can also be used to validate new qPCR assays, test gene primer design, and troubleshoot gene expression data.

Becton Dickinson

201.847.6800

www.bd.com

MJ Research Microseal 96-well semi-skirted microplates

MJ Research is now selling Microseal 96-well semi-skirted microplates designed for use with a wide range of instruments, including both MJ Research and Applied Biosystems thermal cyclers. The full-height wells hold up to 300 µL, and the half-height skirt adds a degree of stiffness to the thin-wall microplates.

MJ Research

888.735.8437

www.mjr.com

Mo Bio Laboratories UltraClean-htp PCR Clean-up Kit

Designed for high-throughput purification of PCR products, the UltraClean kit can purify DNA from 60 bp to 10 kb in size with complete removal of primer dimers up to 50 bp. The kit protocol makes it possible to process one 96-well plate in 15 minutes.

Mo Bio Laboratories

800.606.6246

www.mobio.com

Stratagene StrataScript One-Tube RT-PCR System

The StrataScript One-Tube RT-PCR System with Easy-A PCR cloning enzyme is designed to provide TA/UA cloning in a one-tube RT-PCR format. The system can amplify amplicons up to 5 kb.

Stratagene

800.424.5444

www.stratagene.com

PROTEOMICS

Amersham Biosciences Ni Sepharose Chromatography Medium for His-tagged Proteins

The new pre-charged Ni Sepharose High Performance medium is specifically designed to purify His-tagged proteins. The 34 µm bead matrix is compatible with a wide range of reducing agents, detergents, denaturants, and other additives.

Amersham Biosciences

800.526.3593

www.amershambiosciences.com

Beckman Coulter ProteomeLab IgG Purity/ Heterogeneity Assay

The new ProteomeLab IgG purity and heterogeneity assay is designed to resolve both native and reduced immunoglobulins by size and to quantify the heterogeneity and impurities present. The assay is validated for operation on Beckman’s automated ProteomeLab PA-800 characterization system.

Beckman Coulter

800.742.2345

www.beckmancoulter.com

Eksigent Technologies NanoLC-2D Proteomics System

The new NanoLC-2D system incorporates fully-automated 2-dimensional HPLC separations with a direct pumping nanoscale HPLC system, and employs Eksigent’s microfluidic flow control technology.

Eksigent Technologies

925.960.8869

www.eksigent.com

Eksigent Technologies NanoLC-1D Proteomics System (updated)

The updated NanoLC-1D proteomics system is now compatible with Thermo’s Xcalibur mass spectrometry software system, and a new rapid injection capability allows researchers to load large samples onto trap or analytical columns.

Eksigent Technologies

925.960.8869

www.eksigent.com

Stratagene MS-Grade Trypsin

Stratagene’s MS-grade trypsin consists of porcine pancreas trypsin that is reductively methylated to produce an enzyme that retains activity on exogenous substrates, but is resistant to autolysis. Following treatment with TCPK, an inhibitor of the common contaminant chymotrypsin, the modified, treated trypsin is affinity purified and lyophilized.

Stratagene

800.424.5444

www.stratagene.com

RNAi

BD Biosciences Clontech Knockout RNAi Clone & Confirm PCR Kits

The Knockout RNAi Clone & Confirm PCR kits allow researchers to generate candidate shRNA expression cassettes precloned into vectors in as little as 4.5 hours. The cassettes can also be engineered to co-express a fluorescent marker.

BD Biosciences

800.343.2035

www.bdbiosciences.com

BD Biosciences Clontech RNAi-ready pSIREN Vectors

The pSIREN-RetroQZsGreen and pSIREN-DNR-DsRed-Express vectors provide fluorescent markers for monitoring the delivery efficiency of gene-silencing constructs. Researchers can use fluorescence microscopy to detect cells containing the shRNA vectors, or flow cytometry to enrich for transfected cells.

BD Biosciences

800.343.2035

www.bdbiosciences.com

Dharmacon siSTABLE siRNA

Dharmacon’s siSTABLE siRNA reagents are now available for in vitro cell culture applications to silence expression of genes with low turnover rates, for prolonged silencing, or for use in serum containing culture environments. The proprietary form of siRNA is modified to enhance stability, potency, and silencing longevity.

Dharmacon

800.235.9880

www.dharmacon.com

Panomics TranSilent TF siRNA

Panomics’ TranSilent TF siRNA vectors consist of a mix of up to three different plasmids that target the mRNA of 40 specific human transcription factor genes. These plasmids, each of which has been functionally tested by western blot analysis, encode RNA sequences that are post-transcriptionally converted into siRNA-like transcripts.

Panomics

877.726.6642

www.panomics.com

SAMPLE PREP

BD Biosciences Clontech NucleoSpin Plasmid QuickPure Kit

The new NucleoSpin plasmid QuickPure kits can prepare up to 15 µg of plasmid DNA from 1¯3 ml of bacterial overnight cultures, and can perform multiple mini-preps simultaneously.

BD Biosciences Clontech

877.232.8995

www.bdbiosciences.com

Labnet Compact Microplate Incubator

Labnet’s new Accu-Block Digital Dry Bath provides a compact system for incubating standard 96 well or 384 well microtiter plates. The microtiter block accessory allows the unit to accommodate most plates with a standard SBS footprint.

Labnet

888.522.6381

www.labnetlink.com

Qiagen TissueLyser System

The TissueLyser system from Qiagen can simultaneously disrupt up to 192 biological samples, including animal and plant tissues, bacteria, and yeast. Disruption is achieved through the beating and grinding effect of beads on the sample material as they are shaken with the sample in a variety of grinding vessels.

Qiagen

800.426.8157

www.qiagen.com

Tecan Cellerity Protein Production System

The Cellerity protein production system provides automated cell culture maintenance, cell-line expansion, and harvesting, and is based on Freedom EVO, Tecan’s robotic liquid handling platform.

Tecan

800.832.2687

www.tecan.com

The Automation Partnership Piccolo Automated Protein Production System

Piccolo is a new automated system for the optimization of recombinant protein production in microbial or insect cells. Designed for applications such as structural biology, the system combines incubation with integrated harvesting, lysis, and purification modules.

The Automation Partnership

302.478.9060

www.automationpartnership. com

SNPs AND GENOTYPING

Applied Biosystems SNPlex Genotyping System

The SNPlex genotyping system is designed for genotyping studies using the Applied Biosystems 3730xl and 3730 DNA analyzers. Researchers can genotype 48 SNPs simultaneously in a single biological sample and detect 4,500 SNPs in parallel in as little as 15 minutes.

Applied Biosystems

800.327.3002

www.appliedbiosystems.com

Applied Biosystems GeneMapper Software v3.5 for Accurate Allele Calling

GeneMapper Software v3.5 is designed for allele calling on the ABI PRISM 3100 and 3100-Avant Genetic Analyzers, and the Applied Biosystems 3730 and 3730xl DNA Analyzers.

Applied Biosystems

800.327.3002

www.appliedbiosystems.com/genemapper

Applied Biosystems BioTrekker Software v1.0 for Genotype Management

The BioTrekker software allows multiple users of GeneMapper software v3.5 and the SDS 2.2 Enterprise database to download finished genotyping data in a single results database. The new software supports microsatellite data, data from the SNPlex system and SNaPshot kits analyzed by GeneMapper Software v3.5, and it supports allelic discrimination data from the SDS v2.2 Enterprise database.

Applied Biosystems

800.327.3002

www.appliedbiosystems.com/biotrekker

To tell GT about newly released products, e-mail John MacNeil, senior editor, at [email protected]

The Scan

WHO OKs Emergency Use of Sinopharm Vaccine

The World Health Organization has granted emergency approval for Sinopharm's SARS-CoV-2 vaccine, the Guardian reports.

Scientific Integrity Panel to Meet

According to the Associated Press, a new US scientific integrity panel is to meet later this week.

Trying in the Eye

NPR reports that a study of Editas Medicine's CRISPR therapy for Leber congenital amaurosis has begun.

PLOS Papers on Cerebellum Epigenetics, Copy Number Signature Tool, Acute Lung Injury Networks

In PLOS this week: epigenetics analysis of brain tissue, bioinformatics tool to find copy number signatures in cancer, and more.