Plant Science

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    Quality Control and Preprocessing of Sequencing Reads
    Authors:  Zhiqiang Hao, Xiaojuan Liang and Guanglin Li, date: 07/05/2022, view: 22, Q&A: 0

    Quality control and preprocessing of sequences are essential before analyzing high-throughput sequence data. After raw read data is generated from high-through sequencing platforms, quality control and preprocessing of sequencing reads should

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    Differential Expression Analysis: Simple Pair, Interaction, Time-series
    Authors:  Han Qu, Meng Qu, Shibo Wang, Lei Yu, Qiong Jia, Xuesong Wang and Zhenyu Jia, date: 07/05/2022, view: 29, Q&A: 0

    Identifying differentially expressed (DE) genes across specific conditions is vital in understanding phenotypic variation. The fast-growing RNA sequencing (RNA-seq) provides much information that efficiently quantifies gene expression. Methods and

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    Maize Genome Assembly with PacBio Reads
    Authors:  Ying Hu and Marcio F. R. Resende Jr., date: 07/05/2022, view: 17, Q&A: 0

    Assembly of high-quality genomes is critical for the characterization of structural variations (SV), for the development of a high-resolution map of polymorphisms, and to serve as the foundation for gene annotation. In recent years, the advent

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    GO/KEGG Enrichment Analysis on Gene Lists from Rice (Oryza Sativa)
    Author:  Yahui Li, date: 06/20/2022, view: 81, Q&A: 0

    In RNA-seq data analysis, functional enrichment analysis on genes has become a routine. Many enrichment analysis software and web-applications have emerged. However, gene annotation information is only easily accessible for the most well-studied

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    Quantitative Live Confocal Imaging in Aquilegia Floral Meristems
    Authors:  Ya Min, Stephanie J. Conway and Elena M. Kramer, date: 06/20/2022, view: 992, Q&A: 0

    In this study, we present a detailed protocol for live imaging and quantitative analysis of floral meristem development in Aquilegia coerulea, a member of the buttercup family (Ranunculaceae). Using confocal microscopy and the image analysis

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    Quantitative Analysis of Redox Pool (NAD+, NADH Content) in Plant Samples Under Aluminum Stress
    Authors:  Jay Prakash Awasthi, Bedabrata Saha, Hiroyuki Koyama and Sanjib Kumar Panda, date: 06/20/2022, view: 973, Q&A: 0

    Nicotinamide adenine dinucleotide (NAD) is an essential cofactor of numerous enzymatic reactions found in all living cells. Pyridine nucleotides (NAD+ and NADH) are also key players in signaling through reactive oxygen species (ROS), being crucial

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    Identification of Expression QTL by QTLtools in a Rice Recombinant Inbred Line Population
    Authors:  Feng Xiong, Hu Zhao and Weibo Xie, date: 06/20/2022, view: 122, Q&A: 0

    Expression QTL (eQTL) analysis assesses the association between the expression levels of target genes and genotypes of genetic markers to identify loci that regulate the expression of target genes. eQTL results can be used to construct genetic

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    An Analysis Pipeline for Identification of RNA Modification, Alternative Splicing and Polyadenylation Using Third Generation Sequencing
    Authors:  Yuxiang Liufu, Xuqing Liu, Lin Wu, Hangxiao Zhang, Yubang Gao and Lianfeng Gu, date: 06/05/2022, view: 232, Q&A: 0

    Nanopore sequencing based on Oxford Nanopore Technologies (ONT) and Pacific BioSciences (PacBio) single-molecule real-time (SMRT) long-read isoform sequencing (Iso-Seq) have shown great potential in detecting post-transcriptional regulation. Direct

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    Investigation of Transposon DNA Methylation and Copy Number Variation in Plants Using Southern Hybridisation
    Authors:  Vivek Hari Sundar G. and P. V. Shivaprasad, date: 06/05/2022, view: 504, Q&A: 0

    Plant genomes are pronouncedly enriched in repeat elements such as transposons. These repeats are epigenetically regulated by DNA methylation. Whole genome high-depth sequencing after bisulfite treatment remains an expensive and laborious method to

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    In vitro Assays to Evaluate Specificity and Affinity in Protein-phospholipid Interactions

    Protein–lipid interactions play important roles in many biological processes, including metabolism, signaling, and transport; however, computational and structural analyses often fail to predict such interactions, and determining which lipids

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