Using transposon mutagenesis coupled with high-throughput sequencing, the essential genome of Caulobacter crescentus was determined at 8 bp resolution, including non-coding, regulatory, and coding elements. This high-resolution strategy is applicable to high-throughput, full genome essentiality studies and large-scale genetic perturbation experiments across a broad class of bacterial species.
More...
Christen B, Abeliuk E, Collier JM, Kalogeraki VS, Passarelli B, et al.
The essential genome of a bacterium Mol Syst Biol
Infection of humans with the swine parasite Trichuris suis is reported to cure certain immune diseases. The transcriptome of the T. suis adult stage was examined using next-generation sequencing. A total of 65 million reads were generated, with 17,000 peptides predicted and classified. This analysis provided insights into a number of molecular groups, which are likely to be immuno-regulatory or -modulatory in the infected host.
More...
Cantacessi C, Young ND, Nesjum P, Jex AR, Campbell BE, et al.
The transcriptome of Trichuris suis- first molecular insights into a parasite with curative properties for key immune diseases of humans PLoS One
Using next-generation sequencing, changes in total mRNA from an HIV-infected CD4(+) T cell line were measured, and differences in the expression of both host and viral mRNA were detected. Small changes in T cell activation and other host processes increased near the peak of viral replication, providing new candidate biomarkers of T cell death.
More...
Chang ST, Sova P, Peng X, Weiss J, Law GL, et al.
Next-generation sequencing reveals HIV-1-mediated suppression of T cell activation and RNA processing and regulation of noncoding RNA expression in a CD4+ T cell line Mbio
The Safe-Sequencing System substantially increases the sensitivity of massively parallel sequencing through the addition of a unique identifier (UID) to each template molecule, amplification of molecules to create UID families, and redundant sequencing of the amplification products. Proof of concept was determined by measuring the fidelity of a polymerase, the accuracy of oligonucleotides synthesized in vitro, and the prevalence of mutations in the nuclear and mitochondrial genomes of normal cells.
More...
Kinde I, Wu J, Papadopoulos N, Kinzler KW, Volegstein B
Detection and quantification of rare mutations with massively parallel sequencing Proc Natl Acad Sci USA
Using a long-span, paired-end deep sequencing strategy, cancer genome rearrangements were identified in eight breast cancer genomes, with 40-54% of these structural genomic rearrangements resulting in fusion transcripts, and ~44% of these potentially translated. The fusion transcript RPS6KB1-VMP1 caused by tandem duplication on 17q23 is an indicator of local genomic instability, and is expressed in approximately 30% of breast cancers associated with potential clinical consequences.
More...
Inaki K, Hillmer AM, Ukil L, Yao F, Woo XY, et al.
Transcriptional consequences of genomic structural aberrations in breast cancer Genome Res
Performing expression analysis of complex tissues is complicated by the various component cell types. The authors describe a novel strategy involving single-cell RNA-Seq expression profiles that were clustered to form a two-dimensional cell map onto which expression data were projected. The resulting cell map integrates three levels of organization: the whole population, the functionally distinct subpopulations, and single cells—all without need for known markers to classify cell types.
More...
Islam S, Kjällquist U, Moliner A, Zajac P, Fan JB, et al.
Characterization of the single-cell transcriptional landscape by highly multiplex RNA-Seq Genome Res
Researchers developed a genome assembly algorithm for short-read data from multiple displacement amplification, allowing sequencing of single bacteria cells. The method was demonstrated on an uncultivated marine specimen of Deltaproteobacteria. This novel approach enables acquisition of genome assemblies for individual uncultivated bacteria using only short reads, providing cell-specific genetic information absent from metagenomic studies.
More...
Chitsaz H, Yee-Greenbaum JL, Tesler G, Lombardo MJ, Dupont CL, et al.
Efficient de novo assembly of single-cell bacterial genomes from short-read data sets Nat Biotechnol
The molecular adaptation of Staphylococcus aureus to its host during chronic infection is not well understood. Using comparative genome sequencing, variation in phage content and genetic polymorphisms in genes which influence antibiotic resistance, and global regulation of virulence were revealed in three S. aureus isolates obtained from a cystic fibrosis patient. The identification of genes with this method may inform the design of novel therapeutics for chronic infections.
More...
McAdam PR, Holmes A, Templeton KE, Fitzgerald JR
Adaptive evolution of Staphylococcus aureus during chronic endobronchial infection of a cystic fibrosis patient PLoS One
A metatranscriptome study was performed using the Illumina Genome Analyzer II to investigate the functional diversity of the eukaryotic microorganisms within the rumen of muskoxen (Ovibos moschatus). A much higher percentage of cellulase enzyme discovery and an 8.7x higher rate of total carbohydrate active enzyme discovery per gigabase of sequence was found than in previous rumen metagenomes, providing a snapshot of eukaryotic gene expression, and identifying genes coding for potentially valuable lignocellulolytic enzymes.
More...
Qi M, Wang P, O'Toole N, Barboza PS, Ungerfeld E, et al.
Snapshot of the eukaryotic gene expression in muskoxen rumen- a metatranscriptomic approach PLoS One
Using The HiSeq 2000, a genome sequence was obtained from a 100-year-old lock of hair from an Aboriginal Australian, showing they are descendants of an early human dispersal into eastern Asia, possibly 62,000–75,000 years ago. These findings support the hypothesis that present-day Aboriginal Australians descend from the earliest humans to occupy Australia, likely representing one of the oldest continuous populations outside Africa.
More...
Rasmussen M, Guo X, Wang Y, Lohmueller KE, Rasmussen S, et al.
An Aboriginal Australian genome reveals separate human dispersals into Asia Science
Sequencing - 200G to >20g
HiSeq 2000
Genome Analyzer IIx
MiSeq
Sequencing + Arrays
HiScanSQ
Arrays - Low- to High-Plex
HiScan
iScan
BeadXpress
Real-Time PCR System
Eco Real-Time
