Qi Chen

1 month ago | nature.com | Junchao Shi |Yunfang Zhang |Yun Li |Liwen Zhang |Xudong Zhang |Qi Chen | +2 more

Small noncoding RNAs (sncRNAs) are a diverse group of RNAs including small interfering RNAs, microRNAs, PIWI-interacting RNAs and RNAs derived from structured RNAs such as transfer RNAs, ribosomal RNAs and others. These sncRNAs have varied termini and RNA modifications, which can interfere with adaptor ligation and reverse transcription during cDNA library construction, hindering detection of many types of sncRNA by standard small RNA sequencing methods. To address this limitation, PANDORA sequencing introduces a refined methodology. The procedure includes sequential enzymatic treatments of size-selected RNAs with T4PNK and AlkB, which effectively circumvent the challenges presented by the ligation-blocking termini and reverse transcription-blocking RNA modifications, followed by tailored small RNA library construction protocols and deep sequencing. The obtained datasets are analyzed with the SPORTS pipeline, which can comprehensively analyze various types of sncRNA beyond the traditionally studied classes, to include those derived from various parental RNAs (for example, from transfer RNA and ribosomal RNA), as well as output the locations on the parental RNA from which these sncRNAs are derived. The entire protocol takes ~7 d, depending on the sample size and sequencing turnaround time. PANDORA sequencing provides a transformative tool to further our understanding of the expanding small RNA universe and to explore the uncharted functions of sncRNAs. This Protocol describes optimized procedures for purification and sequencing of small noncoding RNAs from a variety of samples to characterize these diverse RNA species and map them to the parental RNAs from which they originate.

Jan 9, 2025 | science.org | Huachao Zai |Pengfei Yang |Jie Su |Ruiyang Yin |Rundong Fan |Yuetong Wu | +15 more

Dec 31, 2024 | mdpi.com | Qi Chen

5. Discussion 5.1. Numerical Simulation Analysis of Single-Phase Flow Field in the GearboxThis section aims to observe the monophasic flow field within the variable tooth thickness gearbox body. To facilitate subsequent analysis of pressure distribution and airflow movement patterns in the engagement region and its vicinity under different gear speeds and pitch cone angles, this paper establishes two observation planes within the fluid model, as shown in Figure 15.

Dec 11, 2024 | mdpi.com | Qi Chen |Weifeng Zhou |Jian Cheng |Ji Yang

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Dec 10, 2024 | ascpt.onlinelibrary.wiley.com | Yang Xu |Xinyu Li |Qixiang Guo |Qi Chen

CONFLICT OF INTEREST The authors declared no competing interests for this work. Supporting Information Filename Description cpt3511-sup-0001-Supinfo.docxWord 2007 document , 1 MB Appendix S1. Appendix S2. Appendix S3. Appendix S4. Appendix S5. Appendix S6. Table S1. Table S2. Table S3. Table S4. Table S5. Table S6. Table S7. Table S8. Table S9. Table S10. Figure S1. Figure S2. Figure S3. Figure S4.