Next-generation sequencing transforms today's biology

Schuster, Stephan C.

doi:10.1038/nmeth1156

Cited by 1,515 publications

(988 citation statements)

References 19 publications

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“…Different strategies have been used in the past to isolate differentially expressed tissue-specific genes under given biological situations. In recent times, several highthroughput sequencing methods have evolved, which allow reading millions of nucleic acid sequences in short time, thereby expanding the scope of gene discovery beyond what was possible with standard dye terminator methods (Schuster 2008;Tucker et al, 2009). However, SSH as a method was chosen in the current study as it does not require a priori sequence knowledge and can be used with a low quantity of RNA obtained from less abundant tissues such as oocytes and embryos.…”

Section: Discussionmentioning

confidence: 99%

Identification of some unknown transcripts from SSH cDNA library of buffalo follicular oocytes

Rajput

Kumar

Roy

et al. 2013

Animal

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A buffalo oocyte-specific subtracted cDNA library was constructed to identify exclusively or preferentially oocyte-expressed genes. The library represented an enriched population of transcripts obtained from oocytes of diverse ovarian follicular origin and at different stages of in vitro maturation. A total of 1173 high-quality sequences of oocyte-specific genes were clustered into 645 unique sequences, out of which 65.76% were represented as singlets and 34.26% as contig expressed sequence tags (ESTs; clusters). Analysis of sequences revealed that 498 of these sequences were identified as a known sequence in mammalian species including buffalo, 103 as uncharacterized ESTs and 44 unknown sequences including 1 novel EST, so far not reported in any species. Gene ontology annotation classified these sequences into functional categories of cellular events and biological processes associated with oocyte competence. Expression status of the isolated unknown ESTs confirmed that many of these are expressed in oocytes exclusively and in others preferentially, some in excess of 80-fold greater in comparison with a variety of somatic tissues. The isolated novel EST was detected to be expressed exclusively in oocytes and testicular cells only. To our knowledge, this is the first report giving a detailed transcriptome account of oocyte-expressed genes in buffalo. This study will provide important information on the physiological control of oocyte development, as well as many questions yet to be addressed on the reproductive process of buffalo.

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Section: Discussionmentioning

confidence: 99%

Identification of some unknown transcripts from SSH cDNA library of buffalo follicular oocytes

Rajput

Kumar

Roy

et al. 2013

Animal

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“…7 These important characteristics permit the ultra-deep sequencing technologies to be widely used in the field of biology and medical research. NGS technologies have also made a huge and ongoing impact on transcriptome, gene annotation and RNA splice identification in addition to the traditional applications of DNA sequencing in genome resequencing and SNP discovery, Metagenomic 8 and genome methylation analysis 9 have also benefited from these new technologies. A new applications is also likely to be unveiled in the coming years.…”

Section: Introductionmentioning

confidence: 99%

Evaluation of next-generation sequencing software in mapping and assembly

et al. 2011

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Next-generation high-throughput DNA sequencing technologies have advanced progressively in sequence-based genomic research and novel biological applications with the promise of sequencing DNA at unprecedented speed. These new non-Sanger-based technologies feature several advantages when compared with traditional sequencing methods in terms of higher sequencing speed, lower per run cost and higher accuracy. However, reads from next-generation sequencing (NGS) platforms, such as 454/Roche, ABI/SOLiD and Illumina/Solexa, are usually short, thereby restricting the applications of NGS platforms in genome assembly and annotation. We presented an overview of the challenges that these novel technologies meet and particularly illustrated various bioinformatics attempts on mapping and assembly for problem solving. We then compared the performance of several programs in these two fields, and further provided advices on selecting suitable tools for specific biological applications.

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“…This creates a large number of fluorescently labeled DNA molecules to generate enough photons to excite the optical detectors. Second-generation instruments are sold by companies such as 454 Life Sciences, Illumina, and Ion Torrent [7]. Illumina, which was one of the first next-generation device manufacturers, dominates today's market ( figure 1(b)) with various machines such as MiSeq, GAIIx, and HiSeq that target different customer needs such as cost and device performance ( figure 1(c)).…”

Section: First-and Second-generation Sequencing Methodsmentioning

confidence: 99%

The emergence of nanopores in next-generation sequencing

Steinbock¹,

Radenović

2015

Nanotechnology

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Next-generation sequencing methods based on nanopore technology have recently gained considerable attention, mainly because they promise affordable and fast genome sequencing by providing long read lengths (5 kbp) and do not require additional DNA amplification or enzymatic incorporation of modified nucleotides. This permits health care providers and research facilities to decode a genome within hours for less than $1000. This review summarizes past, present, and future DNA sequencing techniques, which are realized by nanopore approaches such as those pursued by Oxford Nanopore Technologies.

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Next-generation sequencing transforms today's biology

Cited by 1,515 publications

References 19 publications

Identification of some unknown transcripts from SSH cDNA library of buffalo follicular oocytes

Identification of some unknown transcripts from SSH cDNA library of buffalo follicular oocytes

Evaluation of next-generation sequencing software in mapping and assembly

The emergence of nanopores in next-generation sequencing

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