Whole-Genome Resequencing

Application Notes

• Whole Genome Resequencing (PDF,382 KB)
• Whole Genome Sequencing of E. Coli Bacteria (PDF, 800 KB)
• Mate-Paired Libraries Detect/Define Genetic Rearrangements (PDF, 530 KB)

Posters

• Genome Variability Analysis of Yoruba in Ibadan, Nigeria (NA18507) by SOLiD Mediated Whole Genome Re-Sequencing (PDF, 278 KB) Ranade, S., et al.
• Next-generation Sequencing for Detection of Rare Variants and Heterozygosity (PDF, 82 KB) (ASHG 2007)
• Finding Indels with Short Sequencing Reads and De Novo Assembly with SOLiD Reads (PDF, 54 KB) Zhang, Z., et al. (ASHG 2007)
• Whole Genome Resequencing with Short Reads: Accurate Mutation Discovery with Mate Pairs and Quality Values ( PDF, 84 KB) McLaughlin, S., et al. (ASHG 2007)
• A high- resolution structural variation map of human germline genomes by next-generation, high-throughput paired end sequencing with the SOLiD™ System (PDF, 154 KB) Peckham, H., et al. (Cold Spring Harbor, Biology of Genomes 2008)

Publications

• Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and Genome analyses. Fullwood et al. Genome Res. 2009 19: 521-532
• The complete genome sequence of Escherichia coli DH10B; insights into the biology of a laboratory workhorse Durfee, T., et al J. of Bacteriology Online 190(7);2597-2606
• Rapid whole- genome mutational profiling using next-generation sequencing technologies, Smith et.al., Genome Res. 2008. 18; 1638-1642
• Comparing Platforms for C. elegans Mutant Identification Using High-Throughput Whole-Genome sequencing. Shen etr al. I (2008)PLoS One 3(12); e4012.doi;10.1371/journal.pone.0004012

Whole Transcriptome Analysis

Posters

• Genome Variability AnalysiS of Yoruba in Ibadan, Nigeria (NA18507) by SOLiD Mediated Whole Genome Re-Sequencing (PDF, 278KB) Ranade, S., et al.
• SOLiD™ Sequencing Unravels Transcriptome. Innovations- Fall 2007
• Single Cell transcriptome Analysis on the SOLiD™ Systems (PDF, 150 KB) Lao, K., et al.

Publications

• mRNA-Seq whole-transcriptome analysis of a single cell.Tang et al, Nature Methods Published on line; 6 April 2009
• The Structure and Complexity of a Bacterial Transcrptome. Passalacqua, K., et al. Bacteriol. 2009; .00122-09v1
• Stem cell transcriptome profiling via massive-scale mRNA sequencing. Cloonan, N.,et al. Nature Methods Online. 2008 Jul; 5 (7); 613-9
• High-Resolution analysis of the 5’-End Transcrptome Using a Next Generation DNA Sequencer. Hashimoto, S.,et al. PLoS ONE 2009;4(1):Epub 2009 Jan 1

Small RNA Analysis

Application Notes

• miRNA Discovery and Profiling with the SOLiD™ Small RNA Expression Kit (PDF, 617 KB)
• Whole Genome Analysis of Small RNA (PDF, 438 KB)

Posters

• A novel approach for miRNA profiling using massively parallel ligation-based sequencing (PDF, 83 KB) Barbacioru, C., et al.

Targeted Resequencing

Application Notes

• Array-based Enrichment of Specific Genomic Regions using the SOLiD™ Systems (PDF, 740 KB)

Posters

• DiBayes: ASNP Detection Algorithm for Next-Generation Dibase Sequencing (PDF, 100 KB) Tang, S., et al.
• Applications of Next Generation Sequencing in Genetic Epidemiology (PDF, 738 KB) De La Vega, F., et al. (ASHG 2007)
• SNP discovery in high-throughput resequenced microarray-enriched human genomic loci (PDF, 300 KB) Antipova, A., et al.

Chromatin Immunoprecipitation (ChIP)

Application Notes

• Chromatin Immunoprecipitation-based Sequencing (ChIP-Seq) on the SOLiD™  System (PDF, 314 KB)

Publications

• Chomatin Immunoprecipitation sequencing (ChIP-Seq) on the SOLiD™ System. Shah et. al. Published online: Nature Methods 6, (2009)
• A high-resolution, nucleosome position map of C.elegans reveals a lack of universal sequence-dictated positioning. Valoeuv, A., et al

Methylation Analysis