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A Method for High-throughput Production of Sequence-verified DNA Libraries and Strain Collections

ABSTRACT: The low costs of array-synthesized oligonucleotide libraries are empowering rapid advances in quantitative and synthetic biology. Unfortunately, high synthesis error rates, uneven representation, and lack of access to individual oligonucleotides limit the true potential of these libraries. We have developed a cost-effective method called Recombinase Directed Indexing (REDI) to address these problems. The method involves integration of a complex library into yeast, site-specific recombination to index (i.e. barcode) library DNA, and then next-generation sequencing to identify clones containing the DNA of interest. We used REDI to generate a molecular probe library (n = ~3,300) that exhibited >96% purity and remarkable uniformity (>95% of probes were within 2-fold relative abundance of the median). Moreover, each sequence-verified probe was readily accessible. We also used REDI to rapidly create an arrayed collection of ~9,000 strains for CRISPR interference in yeast and demonstrate the utility of this collection for highly sensitive phenotypic screening. Our approach will enable a variety of applications requiring accurate, high-quality DNA libraries.

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE81094 | GEO | 2017/02/14

SECONDARY ACCESSION(S): PRJNA320478

REPOSITORIES: GEO

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Project description:DNA methylation assessments of peripheral blood DNA can be used to accurately estimate the relative proportions of underlying leukocyte subtypes. Such cell deconvolution analysis relies on libraries of discriminating differentially methylated regions that are developed for each specific cell type measured. The relationship between estimated cell type proportions can then be tested for their association with phenotypes, disease states, and subject outcomes, or used in multivariable models as terms for adjustment in epigenome-wide association studies (EWAS). We obtained purified neutrophils, monocytes, B-lymphocytes, natural killer (NK) cells, CD4+ T-cells, and CD8+ T-cells from healthy subjects and measured DNA methylation with the Illumina HumanMethylationEPIC array platform. In addition, we measured DNA methylation with the EPIC array in two sets of artificial DNA mixtures comprising the above cell types. We compared three separate approaches to select reference differentially methylated region libraries (DMR library), for cell type proportion inference. The IDOL algorithm identified an optimal DMR library consisting of 450 CpG sites for inferring leukocyte subtype proportions (average R2=99.2). Importantly, the majority of CpG sites (69%) in the IDOL DMR library were unique to the new EPIC methylation array, in that they were not present on the 450K array. Our new reference DMR library is available as a Bioconductor package, has the potential to reduce any unintended technical differences arising from the combination of different generations of array platforms, and may be helpful in generating larger DMR libraries that include novel cell subtypes. A longitudinal dataset of 12 measurements in a single healthy subject (age 33 at the beginning of the blood collection) was used to apply our new DMR library. The subject was followed up for approximately 400 days with samples collected every 40 days. One of the samples was excluded from the final analysis due to a potential mix-up.

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A Method for High-throughput Production of Sequence-verified DNA Libraries and Strain Collections

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