Deep sequencing

Burnside J, Ouyang M, Anderson A et al (2008) Deep sequencing of chicken microRNAs. BMC Genomics 9 185... 

Joyce CE, Zhou X, Xia J et al (2011) Deep sequencing of small RNAs from human skin reveals major alterations in the psoriasis miR-NAome. Hum Mol Genet 20 4025-4040... 

Kozomara A, Griffiths-Jones S (2013) miR-Base annotating high confidence microRNAs using deep sequencing data. Nucleic Acids Res 42 D68-D73... 

Bisulfite conversion followed by PCR amplification and sequencing has become the gold standard in determining patterns of DNA methylation. This method excels over all the others because it allows information about methylation at the base-pair resolution. Nevertheless, until recently, its utilization genome-wide has been slow because bisulfite-based methods are not easily adapted to the array-based hybridization approaches. Yet, bisulfite-converted DNA has been rapidly adapted to cheaper everyday deep-sequencing techniques (Figure 3B). 

Affinity Enrichment ChIP-based methods have been mostly combined with microarrays. These affinity-based techniques are now rapidly shifting to analysis by the next-generation techniques (56,66). As it has been described earlier, DNA immunoprecipitated with the specific methylcytosine antibody is de-cross-linked and defragmented. After ligation with specific probes, the sample is applied for on-site deep sequencing. 

Cons Number of molecules sequenced in a single run is relatively low. Reagents for a sequencing run are approximately twice as costly as those Rate of sequencing errors increase toward the end of the deep sequencing reads Preparation of samples is time-consuming. The di-base color encoding system requires dedicated computational tools for the analysis Homopolymer errors... 

Analysis of Deep Sequencing Data Insights and Challenges... 

How to approach the analysis of billions of short reads of sequence data will vary depending on the question, experimental design, and application of the investigator. Common to any deep sequencing research, however, is the need to first understand the nature and quality of the data that are the basis of all downstream analyses and inferences. 

TABLE 1 Representative Short-Read Mappers for Deep Sequencing Data... 

Deep sequencing application and analysis consist of two basic stages. First is processing the reads, which can be divided into two groupings based on the nucleic acid under consideration DNA-based and RNA-based (Table 2). Read... 

TABLE 2 Summary of DNA- and RNA-Based Deep Sequencing Applications ... 

Identifying the genomic sites that are responsible for gene expression, splicing, posttranscriptional, and other forms of regulation, in cis (i.e., proximal) and in trans (distant), is a critical challenge that deep sequencing is well... 

Several types of heterogeneity exist in deep sequencing experiments, in particularly in RNA-Seq experiments. First, cDNA synthesis via random... 

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