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Unidentified

ABSTRACT: Platform technologies for genome design and synthetic biology (KAP220503)

PROVIDER: PRJDB19430 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	DRR675503_1.fastq.gz	Fastqsanger.gz
	DRR675503_2.fastq.gz	Fastqsanger.gz
	DRR675504_1.fastq.gz	Fastqsanger.gz
	DRR675504_2.fastq.gz	Fastqsanger.gz
	DRR675505_1.fastq.gz	Fastqsanger.gz

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Project description:Sequencing technologies, in particular RNASeq, have become critical tools in the design, build, test, learn cycle for synthetic biology. They provide a better understanding of synthetic designs and they help identify ways to improve and select designs. While this data is beneficial to design, its collection and analysis is a complex, multi-step process that has implications both on discovery and reproducibility of experiments. Additionally, tool parameters, experimental metadata, and normalization of data and standardization of file formats present challenges that are computationally intensive. This calls for high-throughput pipelines expressly designed to handle the combinatorial and longitudinal nature of synthetic biology. In this paper, we present a pipeline to maximize analytical reproducibility of RNASeq for synthetic biologists. We also explore the impact of reproducibility on the validation of machine learning models.

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Project description:The phi X 174 bacteriophage was first sequenced in 1977, and has since become the most widely used standard in molecular biology and next-generation sequencing. However, with the advent of affordable DNA synthesis and de novo gene design, we considered whether we could engineer a synthetic genome, termed SynX, specifically tailored for use as a universal molecular standard. The SynX genome encodes 21 synthetic genes that can be in vitro transcribed to generate matched mRNA controls, and in vitro translated to generate matched protein controls. This enables the use of SynX as a matched control to compare across genomic, transcriptomic and proteomic experiments. The synthetic genes provide qualitative controls that measure sequencing accuracy across k-mers, GC-rich and repeat sequences, as well as act as quantitative controls that measure sensitivity and quantitative accuracy. We show how the SynX genome can measure DNA sequencing, evaluate gene expression in RNA sequencing experiments, or quantify proteins in mass spectrometry. Unlike previous spike-in controls, the SynX DNA, RNA and protein controls can be independently and sustainably prepared by recipient laboratories using common molecular biology techniques, and widely shared as a universal molecular standard.

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