Browsing by Author "Lin, Wei-Chen"

Now showing 1 - 5 of 5

Evaluation and Application of the Strand-Specific Protocol for Next-Generation Sequencing
(2015-01-01)
Tsai, Kuo-Wang
;
Chang, Bill
;
Pan, Cheng-Tsung
;
Lin, Wei-Chen
;
Chen, Ting-Wen
Next-generation sequencing (NGS) has become a powerful sequencing tool, applied in a wide range of biological studies. However, the traditional sample preparation protocol for NGS is non-strand-specific (NSS), leading to biased estimates of expression for transcripts overlapped at the antisense strand. Strand-specific (SS) protocols have recently been developed. In this study, we prepared the same RNA sample by using the SS and NSS protocols, followed by sequencing with Illumina HiSeq platform. Using real-time quantitative PCR as a standard, we first proved that the SS protocol more precisely estimates gene expressions compared with the NSS protocol, particularly for those overlapped at the antisense strand. In addition, we also showed that the sequence reads from the SS protocol are comparable with those from conventional NSS protocols in many aspects. Finally, we also mapped a fraction of sequence reads back to the antisense strand of the known genes, originally without annotated genes located. Using sequence assembly and PCR validation, we succeeded in identifying and characterizing the novel antisense genes. Our results show that the SS protocol performs more accurately than the traditional NSS protocol and can be applied in future studies.
miRSeq: A User-Friendly Standalone Toolkit for Sequencing Quality Evaluation and miRNA Profiling
(2014)
Pan, Cheng-Tsung
;
Tsai, Kuo-Wang
;
Hung, Tzu-Min
;
Lin, Wei-Chen
;
Pan, Chao-Yu
MicroRNAs (miRNAs) present diverse regulatory functions in a wide range of biological activities. Studies on miRNA functions generally depend on determining miRNA expression profiles between libraries by using a next-generation sequencing (NGS) platform. Currently, several online web services are developed to provide small RNANGS data analysis. However, the submission of large amounts of NGS data, conversion of data format, and limited availability of species bring problems. In this study, we developed miRSeq to provide alternatives. To test the performance, we had small RNA NGS data from four species, including human, rat, fly, and nematode, analyzed with miRSeq. The alignments results indicate that miRSeq can precisely evaluate the sequencing quality of samples regarding percentage of self-ligation read, read length distribution, and read category. miRSeq is a user-friendly standalone toolkit featuring a graphical user interface (GUI). After a simple installation, users can easily operate miRSeq on a PC or laptop by using a mouse. Within minutes, miRSeq yields useful miRNA data, including miRNA expression profiles, 3\' end modification patterns, and isomiR forms. Moreover, miRSeq supports the analysis of up to 105 animal species, providing higher flexibility.
Reduction of interstrand charge repulsion of DNA duplexes by salts and by neutral phosphotriesters - Contrary effects for harnessing duplex formation
(2020-05-01)
Kuo, Tai-Chih
;
Wu, Meng-Wei
;
Lin, Wei-Chen
;
Matulis, Daumantas
;
Yang, Yuh-Shyong
To exploit the formation of DNA duplexes, the charge repulsion between complementary DNA strands can be reduced by adding salts or by replacing the negatively charged natural phosphodiester linkage( s) with charge-neutral methyl phosphotriester(s) (MPTE) linkage( s) of the synthetic nDNA oligonucleotides. Recently, we reported prominent improvements of detecting target nucleic acids with nDNA probes on liquid-phase PCR and solid/liquid-interface biosensing. To understand the observed improvements from thermodynamics perspectives, we studied the formation and stability of the double-stranded DNA (dsDNA) containing nDNA and/or natural DNA. With the natural DNA oligonucleotides, increment of Na+ cations caused unexpected reductions of favorable enthaply (Delta H) of duplex formation and expected increases of favorable free energy (Delta G) and temperature of melting transition (T-m). With one nDNA in duplex formation, the increase of Na+ yielded extra faborable Delta H, yet unfavorable Delta G and T-m . Possibly, Na(+ )cations ( > 50 mM) promote the formation of dsDNA through the endothermic release of DNA (and nDNA)-hydrating water molecules more than through the reduction of inter-strand repulsions. The methyl groups of MPTE of nDNA also destabilize the DNA duplexes by hindering the formation of standard double helices. These novel findings explain the duplex-destabilization property of nDNA which enables its discrimination of single-nucleotide polymorphisms. (C) 2020 Taiwan Institute of Chemical Engineers. Published by Elsevier B.V. All rights reserved.
Single-Step Per-O-Sulfonation of Sugar Oligomers with Concomitant 1,6-Anhydro Bridge Formation for Binding Fibroblast Growth Factors
(2019-01-18)
Yeh, Che-Jui
;
Ku, Chiao-Chu
;
Lin, Wei-Chen
;
Fan, Chiao-Yuan
;
Zulueta, Medel Manuel L.
Many circulating cancer-related proteins, such as fibroblast growth factors (FGFs), associate with glycosaminoglycans-particularly heparan sulfate-at the cell surface. Disaccharide analogues of heparan sulfate had previously been identified as the shortest components out of the sugars that bind to FGF-1 and FGF-2. Taking note of the typical pose of l-iduronic acid, we conceived of per-O-sulfonated analogues of such disaccharides, and devised a single-step procedure for per-O-sulfonation of unprotected sugars with concomitant 1,6-anhydro bridge formation to achieve such compounds through direct use of SO3Et3N as sulfonation reagent and dimethylformamide as solvent. The synthesized sugars based on the oligomaltose backbone bound FGF-1 and FGF-2 mostly at the sub-micromolar level, although the tetrasaccharide analogue achieved low-nanomolar binding with FGF-2.
Synthesis of Petal-Like Carbon Nanocapsule@MnO2 Core-Shell Particles and Their Application in Supercapacitors
(2014)
Lee, Ting-Ting
;
Hong, Jing-Ru
;
Lin, Wei-Chen
;
Hu, Chi-Chang
;
Wu, Pu-Wei
Carbon nanocapsule (CNC)@MnO2 core-shell particles are prepared with a reaction of KMnO4 with CNC at 90 degrees C. Birnessite-type MnO2 nanoflakes are grown on CNC seeds, resulting in CNC@MnO2 particles with a petal-like structure. The electrochemical characteristics of the prepared materials show that the highest specific capacitance (163 Fg(-1)) was obtained with a scan rate of 2 mVs(-1) in 1 M Na2SO4. In addition, the synthesized material has superior cycling stability. The capacitance retains 97.8% of its initial value after 5000 cycles with a scan rate of 100 mVs(-1). (C) 2014 The Electrochemical Society. All rights reserved.