Plant Science


    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: 116, 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

    Transformation, Normalization, and Batch Effect Removal
    Authors:  Lei Yu, Han Qu, Qiong Jia, Xuesong Wang and Zhenyu Jia, date: 07/20/2022, view: 107, 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

    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

    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

    Quality Control and Preprocessing of Sequencing Reads
    Authors:  Zhiqiang Hao, Xiaojuan Liang and Guanglin Li, date: 07/05/2022, view: 235, 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

    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

    Quantitative Live Confocal Imaging in Aquilegia Floral Meristems
    Authors:  Ya Min, Stephanie J. Conway and Elena M. Kramer, date: 06/20/2022, view: 1223, 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

    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: 1226, 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

    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

    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: 405, 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


    We use cookies on this site to enhance your user experience. By using our website, you are agreeing to allow the storage of cookies on your computer.