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
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
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
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 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
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
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
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
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
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