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Applied Biosystems: The SOLID Read

Issue 4: July 2009

IN THE NEWS

PUBLICATIONS

RESEARCHER SPOTLIGHT

Applied Biosystems Launches Sequencing-based Solution to Advance Whole Transcriptome Research
Scientists from Applied Biosystems First to Sequence Entire Human Genome in Single Run at 17-fold Coverage
Applied Biosystems and Geospiza Team Up to Offer Next-Generation Genetic Analysis on Amazon Web Services
Applied Biosystems Scientists Use Next-Generation Sequencing to Associate Methylation Patterns with the Development of Cancer
Scientists Use Advanced Genomic Technology from Applied Biosystems to Uncover Profiles of Gene Activity from Single Cells

Preparation of genome-wide DNA fragment libraries using bisulfite in polyacrylamide gel electrophoresis slices with formamide denaturation and quality control for massively parallel sequencing by oligonucleotide ligation and detection
Ranade, S. S., et al. Anal Biochem. 2009 Jul 15; 390(2):126–35. DOI:10.1016/j.ab.2009.04.020
Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two base encoding
McKernan, K. J., et al. Genome Res. Advance online publication June 22, 2009. DOI: 10.1101/gr.091868.109
Limitations and possibilities of small RNA digital gene expression profiling
Linsen et al. Nature Methods 6, 474–476 (30 June 2009) doi:10.1038/nmeth0709–47.

Dr. Greg Foltz and Dr. Anup Madan,
co-directors of the Center for Advanced Brain Tumor Treatment at the Swedish Neuroscience Institute

We recently had the opportunity to talk with Dr. Madan and Dr. Foltz about the collaborative work they are doing, and how Applied Biosystems is helping scientists and physicians better understand the genomics of brain tumors and more effectively treat the patients afflicted by them.
LEARN MORE>

Dear Researcher,

Welcome to the July 2009 issue of THE SOLID Read, the eNewsletter dedicated to delivering you the latest scientific and technical advances made with the SOLiD™ System. Highlights in this issue include new information on The SOLiD™ 3 System, an interview with Anup Madan and Greg Foltz of the Swedish Neuroscience Institute, and upcoming events featuring the SOLiD™ System.

PRODUCT UPDATES

	Reagent Kits—Always high quality, formulated for optimal performance, and ease-of-use. New SOLiD™ Sample Preparation Kits SOLiD™ Whole Transcriptome Analysis Kit—Discover something new in RNA. Rapid construction of strand-specific libraries from total RNA, ribosomal depleted total RNA, or Poly(A+) RNA. SOLiD™ SAGE™—An optimized solution for generating up to 8 libraries of 3' expression tags averaging 27 bp to enable the digital enumeration of gene expression profiles on the SOLiD™ System. New SOLiD™ Library Preparation Kits SOLiD™ 2 x 25 bp Mate-Paired Library Construction Kit—for generation of 2 x 25 bp mate-paired libraries with 600 bp to 6 kb inserts SOLiD™ Long Mate-Paired Library Construction Kit—for generation of 2 x 35 bp or longer mate-paired libraries with 600 bp to 6 kb inserts New SOLiD™ Sequencing Master Mix SOLiD™ Fragment Library Sequencing Kit—Master Mix 35 is the ideal kit for small RNA applications

SOFTWARE DEVELOPMENT COMMUNITY UPDATES

	Visit the SOLiD Development Community to access the new data analysis resources described below. Applied Biosystems Software Base Sequence Conversion Tool: SOLiD™ BASEQV Tool: Tool for the conversion of SOLiD™ System output files to base-sequence data in SAM format with associated quality values (QV). Whole Transcriptome Analysis: AB WT Analysis Pipeline updated: The pipeline now supports novel-transcript identification and mapping over splice junctions. SOLiD™ SAGE™ Analysis Software released: A tool for taking the raw sequence data files generated from using the SOLiD™ SAGE™ Kit and matching them to known sequences in your reference database of choice. Resequencing: AB CNV Tool: A software tool for detecting CNVs for human SOLiD™ sequencing data from fragment or mate-pair libraries. AB diBayes SNP Tool: A software tool for detecting SNPs with SOLiD™ sequencing data. AB Large InDel Tool: A software tool for detecting large InDels in SOLiD™ sequencing data. AB Small InDel Tool: Improved algorithm for detecting small InDels. AB Inversion Tool: Now supports small inversion. SOLiD™ System Analysis Pipeline Tool (Corona Lite): Update includes inversion detection, SGE job management support and improved mapping. SOLiD™ System Color Space Mapping Tool (mapreads): Improved algorithm for mapping. New Academic Tools Resequencing: CNV-Seq: Implementation of a new method to detect CNVs using high-throughput sequencing, published in BMC Bioinformatics 2009, 10:80. Register here to receive updates and new software release announcements.

WEBINARS (Registration Required)

	mRNA-Seq Analysis of a Single Cell Whole Transcriptome Analysis Advances in Cancer Genomics

EVENTS

	SOLiD™ System North and Latin America User Group Meeting September 9–12 2009 \| California, USA American Society for Human Genetics (ASHG) October 20–24 2009 \| Honolulu, Hawaii USA


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