Low-Bias Manipulation of DNA Oligo Pool for Robust Data Storage

Gao, Yanmin; Chen, Xin; Qiao, Hongyan; Ke, Yonggang; Qi, Hao

doi:10.1021/acssynbio.0c00419

Cited by 26 publications

(19 citation statements)

References 25 publications

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“…To assess the ampli cation bias, the DNA master pool 1 containing 11520 DNA strands previously prepared in our laboratory was used in this study (Gao et al, 2020). To reduce or eliminate the impact of different primers on the priming e ciency, all 11520 oligos used the same forward and reverse primers.…”

Section: Oligo Pool For Deep Replicationmentioning

confidence: 99%

Oligo replication advantage driven by GC content and Gibbs free energy

et al. 2022

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Large scale DNA oligo pools are emerging as a novel material in a variety of advanced applications.However, GC content and length cause signi cant bias in ampli cation of oligos. We systematically explored the ampli cation of one oligo pool comprising of over ten thousand distinct strands with moderate GC content in the range of 35-65%. Uniqual ampli cation of oligos result to the increased Gini index of the oligo distribution while a few oligos greatly increased their proportion after 60 cycles of PCR. However, the signi cantly enriched oligos all have relatively high GC content. Further thermodynamic analysis demonstrated that a high value of both GC content and Gibbs free energy could improve the replication of speci c oligos during biased ampli cation. Therefore, this double-G (GC content and Gibbs free energy) driven replication advantage can be used as a guiding principle for the sequence design for a variety of applications, particularly for data storage.

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Section: Oligo Pool For Deep Replicationmentioning

confidence: 99%

Oligo replication advantage driven by GC content and Gibbs free energy

et al. 2022

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“…The raw CEL data of GSE132176 and GSE141955 were downloaded along with the corresponding annotation platform files. Subsequently, the "Oligo, " "robust multi-array analysis (RMA), " and "linear models for microarrays (LIMMA)" algorithms were applied to analyze the microchip raw data (14)(15)(16). The overall process was as follows: (1) perform data background processing, normalization, and gene expression acquisition; (2) filter the "non-expressed" gene/probe expression data, in which the probe with a p-value <0.05 was selected based on the "paCalls" method; (3) obtain the probe information and convert the expression value following the "getProbeInfo" method; and (4) perform a differentially expressed gene (DEG) analysis via the "LIMMA" algorithm, in which the DEGs with criteria of the Benjamini-Hochberg method corrected a p-value <0.05 and log2-fold change (FC) >1.0.…”

Section: Data Acquisitionmentioning

confidence: 99%

Circular Network of Coregulated Sphingolipids Dictates Chronic Hypoxia Damage in Patients With Tetralogy of Fallot

Zhou

Liu

Zou

et al. 2022

Front. Cardiovasc. Med.

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Background: Tetralogy of Fallot (TOF) is the most common cyanotic heart disease. However, the association of cardiac metabolic reprogramming changes and underlying molecular mechanisms in TOF-related chronic myocardial hypoxia damage are still unclear.Methods: In this study, we combined microarray transcriptomics analysis with liquid chromatography tandem-mass spectrometry (LC–MS/MS) spectrum metabolomics analysis to establish the metabolic reprogramming that occurs in response to chronic hypoxia damage. Two Gene Expression Omnibus (GEO) datasets, GSE132176 and GSE141955, were downloaded to analyze the metabolic pathway in TOF. Then, a metabolomics analysis of the clinical samples (right atrial tissue and plasma) was performed. Additionally, an association analysis between differential metabolites and clinical phenotypes was performed. Next, four key genes related to sphingomyelin metabolism were screened and their expression was validated by real-time quantitative PCR (QT-PCR).Results: The gene set enrichment analysis (GSEA) showed that sphingolipid metabolism was downregulated in TOF and the metabolomics analysis showed that multiple sphingolipids were dysregulated. Additionally, genes related to sphingomyelin metabolism were identified. We found that four core genes, UDP-Glucose Ceramide Glucosyltransferase (UGCG), Sphingosine-1-Phosphate Phosphatase 2 (SGPP2), Fatty Acid 2-Hydroxylase (FA2H), and Sphingosine-1-Phosphate Phosphatase 1 (SGPP1), were downregulated in TOF.Conclusion: Sphingolipid metabolism was downregulated in TOF; however, the detailed mechanism needs further investigation.

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“…The validation dataset GSE169214 was downloaded in response to the hypoxic or normoxic environment of the cardiac tissue in the mouse model for cyanotic congenital heart disease. The "Oligo" algorithm was used for raw data preprocessing (26). Consequently, the online version of ToppGene Suite (https://toppgene.cchmc.org/) was used for hub gene functional enrichment (27).…”

Section: Hub Regulators and Functional Detectionmentioning

confidence: 99%

Metabolic Variation Dictates Cardiac Pathogenesis in Patients With Tetralogy of Fallot

et al. 2022

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BackgroundHerein, we aimed to analyze cardiac metabolic reprogramming in patients with tetralogy of Fallot (ToF).MethodsCardiac metabolic reprogramming was analyzed through comprehensive bioinformatics analysis, which included gene set enrichment, gene set variation, and consensus clustering analyses, so as to assess changes in metabolic pathways. In addition, full-spectrum metabolomics analysis was performed using right atrial biopsy samples obtained from patients with ToF and atrial septal defect (ASD) before cardiopulmonary bypass; ultrahigh performance liquid chromatography–tandem mass spectrometry (UPLC–MS/MS) was used to construct a metabolic map of cardiac metabolic reprogramming in cyanotic congenital heart disease.ResultsThe metabolic maps of carbohydrate metabolic process and heme metabolism were significantly activated, while bile acid metabolism, lipid droplet, and lipid binding were primarily restrained in ToF samples as compared with that in ASD samples. The reprogramming of butanoate metabolism was identified basing on the UPLC–MS/MS detection and analysis in myocardial hypoxia damage in cyanotic heart disease. Finally, the butanoate metabolism–related hub regulators ALDH5A1 and EHHADH were identified and they were significantly downregulated in ToF samples.ConclusionsThe metabolic network of butanoate metabolism involved ALDH5A1 and EHHADH, which could contribute to myocardial tissue damage in cyanotic congenital heart of ToF. Our results provide further insights into the mechanisms underlying metabolic reprogramming in cyanotic congenital heart disease and could lead to the identification of potential therapeutic targets.

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Low-Bias Manipulation of DNA Oligo Pool for Robust Data Storage

Cited by 26 publications

References 25 publications

Oligo replication advantage driven by GC content and Gibbs free energy

Oligo replication advantage driven by GC content and Gibbs free energy

Circular Network of Coregulated Sphingolipids Dictates Chronic Hypoxia Damage in Patients With Tetralogy of Fallot

Metabolic Variation Dictates Cardiac Pathogenesis in Patients With Tetralogy of Fallot

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