Plant Science

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    Contigs Scaffolding with Hi-C for Plant Genomes
    Authors:  Hong An, Qing Xiao, Zhibo Jia, J. Chris Pires and Bin Yi, date: 08/05/2022, view: 118, Q&A: 0

    Hi-C is a chromosome conformation capture method originally developed to detect genome-wide chromatin interactions. Nowadays, it is widely applied in scaffolding de novo assembled contigs into chromosome-scale genome sequences. Multiple open-source

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    Transformation, Normalization, and Batch Effect Removal
    Authors:  Lei Yu, Han Qu, Qiong Jia, Xuesong Wang and Zhenyu Jia, date: 07/20/2022, view: 109, Q&A: 0

    In bulk RNA-seq analysis, normalization and batch effect removal are two procedures necessary to scale the read counts and reduce technical errors. Many differential expression analysis tools require a raw count matrix as input and embed the

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    Quality Control and Preprocessing of Sequencing Reads
    Authors:  Zhiqiang Hao, Xiaojuan Liang and Guanglin Li, date: 07/05/2022, view: 238, 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: 204, 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: 152, 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: 202, 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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    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: 235, 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: 407, 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: 717, 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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    Application of Cadaverine to Inhibit Biotin Biosynthesis in Plants
    Authors:  Nicole M. Gibbs, Shih-Heng Su and Patrick H. Masson, date: 04/20/2022, view: 671, Q&A: 0

    Biotin is an essential vitamin in plants. However, characterization of biotin deficiency has been limited by embryo lethality in mutants, which can only be rescued by supplementation of biotin. Here, we describe a protocol to characterize

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