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Dear Researcher, Welcome to the April 2009 issue of THE SOLID Read, the eNewsletter dedicated to delivering the latest scientific and technical advances made with the SOLiD™ System. Highlights in this issue include information on the SOLiD™ 3 System, an interview with Alain Nicolas of the Institut Curie, and upcoming events featuring the SOLiD System. |
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IN THE NEWS
 PRODUCT UPDATES |
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SOLiD Commercial Software Updates With the launch of the SOLiD 3 System, the GlobalSETS software is now available for offline (off-instrument) data analysis. It comes with a resequencing analysis pipeline and provides the SOLiD Applications Interface (SAI) for integrating a custom analysis pipeline. This commercial bioinformatics software provides robust performance and new features for data analysis. More Info > SOLiD 3 System Sequencing Kits and Reagents  SOLiD Fragment Library Construction Kit with Invitrogen™ E-Gel® SizeSelect™ Gels—Now Available
The SOLiD Fragment Library Construction Kit with SizeSelect™ Gels provides a fully optimized, complete set of reagents, columns, and SizeSelect gels to generate 10 fragment libraries using the SOLiD System. More Info > SOLiD Fragment Library Construction Reagents
The SOLiD Fragment Library Construction Reagents comprise a fully optimized set of reagents to generate 10 fragment libraries using the SOLiD standard or express fragment library protocols. More Info > SOLiD Fragment Library Construction Kit
The SOLiD Fragment Library Construction Kit provides a fully optimized set of reagents and columns to generate 10 fragment libraries using the SOLiD express fragment library protocol. More Info > Application-Specific Kits and Reagents Whole Transcriptome Protocol—NOW AvailableMore Info > MethylMiner™ Methylated DNA Enrichment Kit
The MethylMiner™ Methylated DNA Enrichment Kit delivers highly sensitive enrichment of methylated DNA for downstream analysis including SOLID sequencing and PCR-and qPCR-based assays. More Info > MAGnify™ Chromatin Immunoprecipitation System
Reagents and antibodies for ChIP with sequence analysis validated on the SOLiD System. More Info > |
Software Development Community Updates Visit the SOLiD Development Community to access the new data analysis resources described below. More Info > New Applied Biosystems Tools Available for Whole Transcriptome Analysis and Gene Expression Analysis
• AB WT Analysis Pipeline: Currently our pipeline supports functionality for mapping SOLiD System reads from a transcript sample to a reference genome and for assigning tag counts to features of the reference genome. New Academic Tools for Sequence Alignment
• ADiR: An assembler for color space reads that makes use of color transition properties in resolving overlap and consensus. • RNA-MATE: RNA-MATE is a computational pipeline based on a recursive mapping strategy for placing strand-specific RNAseq data onto a reference genome. This pipeline provides an automatic and integrated way to align color space sequencing data, collate this information, and generate files for examining gene expression data in a genomic context. Partnership Updates
• New Member—Partek: Partek is the maker of Partek Genomics Suite™ software designed to easily analyze and compare gene expression, digital gene expression, exon expression, human gene ST, association studies/copy number analysis, and regulation/ChIP-chip, ChIP-Seq data. • New Member—CLC Bio: CLC Bio just released a comprehensive suite of software applications which supports assembly of SOLiD data in native color space and graphical viewing of color space, as well as downstream analysis. All of CLC Bio's products incorporate high-performance computing-based algorithms for extremely fast assembly and for easy integration with a typical next-generation sequencing workflow. • New Member—Genologics: Genologics provides Geneus, which enables end-to-end lab and data management for next-generation sequencing labs using the SOLiD System. It is a highly flexible and configurable LIMS and data pipelining system, which allows you to plug in command line–driven analysis tools of your choice. Geneus fully supports SOLiD System applications including whole genome resequencing, de novo sequencing, targeted resequencing, gene expression profiling, small RNA analysis, whole transcriptome analysis, ChIP sequencing, and methylation analysis. Register here to receive updates and new software release announcements.
New SOLiD System Training Centre, Darmstadt Germany Training expertise in the heart of Europe—the Training Centre welcomes customers for workshops, and training courses for the SOLiD 3 System, now extended with new courses. |
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| EVENTS |
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| American Association for Cancer Research
April 18–22, 2009 | Denver, CO, USA GeneMappers 2009 Conference
April 14–17, 2009 | Blue Mountains World Heritage Region, NSW, Australia Molecular Systems Biology of the Cell
April 20, 2009 | Seattle, WA, USA European Human Genetics Conference
May 23–26, 2009 | Vienna, Austria Science Webinar Series: Advances in Cancer Genomics
April 30, 2009 | 12 p.m. Eastern, 9 a.m. Pacific, 4 p.m. GMT Learn More > Genetics of Complex Diseases and Isolated Populations
May 26–29, 2009 | Trieste, Italy European SOLiD System Users Meeting
June 10–11, 2009 | Milan, Italy |
ISMB/ECCB 2009 (Intelligent Systems for Molecular Biology/European Conference on Computational Biology) June 27–July 2, 2009 | Stockholm, Sweden
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