In general, we aim for 10 × 10 6 unique reads for each ChIP-seq, which is in accordance with the recently published recommendations from the ENCODE project ( Landt et al., 2012). It has been shown that the number of positive target sites identified by ChIP-seq in general increases with the amount of sequencing reads ( Myers et al., 2011). The Illumina sequencing technology, including technical aspects and biochemistry, has been described previously ( Bentley et al., 2008). Ronni Nielsen, Susanne Mandrup, in Methods in Enzymology, 2014 2.3.8 Illumina sequencing Illumina sequencing has been successfully applied in the characterization of structure and composition of microbial communities in coking wastewater treatment plants ( Ma et al., 2015), metagenomic profiling of antibiotic resistance genes and mobile genetic elements in a tannery wastewater treatment plant ( Wang et al., 2013), metagenomic insight of nitrogen metabolism in a tannery wastewater treatment plant with bioaugmented microbial consortium ( Sul et al., 2016), tracking of dynamics of soil bacterial community during bioremediation of pollutants ( Deng et al., 2016), and identification of potential microbial agents for bioremediation ( Hong et al., 2017). Additionally, this method only uses DNA polymerase as opposed to multiple, expensive enzymes required by other sequencing techniques (i.e., pyrosequencing). Due to the automated nature of Illumina dye sequencing, it is possible to sequence multiple strands at once and gain actual sequencing data quickly. This technique offers a number of advantages over traditional sequencing methods such as Sanger sequencing. The workflow and all the steps of Illumina sequencing can be found elsewhere ( ). Illumina offers a full portfolio of sequencing platforms, from the benchtop MiniSeq and MiSeq Systems to the large-scale HiSeq X and NovaSeq series of sequencing systems that deliver the right level of speed, capacity, and cost for various laboratories or sequencing requirements with user-friendly bioinformatics tools that are easily accessible through the web, on instrument, or through on-site servers ( ). The innovative and flexible sequencing system enables a broad array of applications in genomics, transcriptomics, and epigenomics. It can also be used for whole-genome and region sequencing transcriptome analysis, sRNA discovery, methylation profiling, and genome-wide protein–nucleic acid interaction analysis. This sequencing method is based on reversible dye-terminators that enable the identification of single bases as they are introduced into DNA strands. It was developed by Shankar Balasubramanian and David Klenerman of Cambridge University, who subsequently founded Solexa, a company later acquired by Illumina. Illumina dye sequencing is a molecular technique used to determine the series of base pairs in DNA, also known as DNA sequencing. Mulla, in Microbial Diversity in the Genomic Era, 2019 26.4.5.1 Illumina Sequencing
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