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Inference of Ancient Polyploidy Using Transcriptome Data
Polyploidizations, or whole-genome duplications (WGDs), in plants have increased biological complexity, facilitated evolutionary innovation, and...
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Bioinformatics Methods for Transcriptome Analysis on Teratogenesis Testing
Teratogenesis testing can be challenging due to the limitations of both in vitro and in vivo models. Test-systems, based especially on human...
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Phylogenetic analysis of Lamiaceae based on transcriptome data
The Lamiaceae family is included in the angiosperms and comprises over 7000 species, many of which are of considerable ecological, economic, and...
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Integrating Single-Cell Methylome and Transcriptome Data with MAPLE
As a mechanism of epigenetic gene regulation, DNA methylation has crucial roles in developmental and differentiation programs. Thanks to the recently...
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Transcriptome Data Analysis Using a De Novo Assembly Approach
Characterization and profiling of the gene expression data or, more formally, called transcriptome are crucial steps in revealing the involvement of...
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Transcriptome analysis in abiotic stress conditions in higher plants
Drought, high salinity, and low temperature are major environmental factors that limit plant productivity. Plants respond and adapt to these stresses...
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Single Cell Transcriptome Analysis During Development in Dictyostelium
Dictyostelium represents a stripped-down model for understanding how cells make decisions during development. The complete life cycle takes around a...
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RNA-Seq Data Analysis Pipeline for Plants: Transcriptome Assembly, Alignment, and Differential Expression Analysis
In this chapter, we describe methods for analyzing RNA-Seq data, presented as a flow along a pipeline beginning with raw data from a sequencer and...
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Transcriptome Analysis of Aquatic Species Exposed to Endocrine Disruptors
Animals and humans both have normal endocrine systems that are affected by endocrine-disrupting chemicals (EDCs). Numerous substances found in...
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Analysis of the Plant Mitochondrial Transcriptome
Transcriptome analyses are widely performed, but the analysis of organelle genome expression is often overlooked. In this chapter, we describe three...
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Multi-slice spatial transcriptome domain analysis with SpaDo
With the rapid advancements in spatial transcriptome sequencing, multiple tissue slices are now available, enabling the integration and...
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Transcriptome-Wide Analysis of mRNA Adenylation Status in Yeast Using Nanopore Sequencing
There are multiple methods for studying deadenylation, either in vitro or in vivo, which allow for observation of mRNA abundance or poly(A) tail...
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Finger Millet Transcriptome Analysis Using High Throughput Sequencing Technologies
During the past two decades, high-throughput transcriptome sequencing has developed into a well-established and widely used research method....
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Split Pool Ligation-based Single-cell Transcriptome sequencing (SPLiT-seq) data processing pipeline comparison
BackgroundSingle-cell sequencing techniques are revolutionizing every field of biology by providing the ability to measure the abundance of...
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Integrative analysis of Iso-Seq and RNA-seq data reveals transcriptome complexity and differential isoform in skin tissues of different hair length Yak
BackgroundThe hair follicle development process is regulated by sophisticated genes and signaling networks, and the hair grows from the hair...
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Analysis of Single-Cell Transcriptome Data in Drosophila
The fly Drosophila is a versatile model organism that has led to fascinating biological discoveries. In the past few years, Drosophila researchers...
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Targeting nucleotide metabolic pathways in colorectal cancer by integrating scRNA-seq, spatial transcriptome, and bulk RNA-seq data
BackgroundColorectal cancer is a malignant tumor of the digestive system originating from abnormal cell proliferation in the colon or rectum, often...
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Transcriptome Sequencing and Analysis of Seabuckthorn (Hippophae Sp.)
Seabuckthorn (Hippophae Sp.) is known for its immense medicinal, nutritional, and agronomical properties and has been utilized for centuries as...
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Analysis of ROS-Triggered Changes in the Transcriptome
RNA sequencing is routinely used for determining transcriptome-wide expression changes during various conditions, including oxidative stress...
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Definition of the transcriptional units of inherited retinal disease genes by meta-analysis of human retinal transcriptome data
BackgroundInherited retinal diseases (IRD) are genetically heterogeneous disorders that cause the dysfunction or loss of photoreceptor cells and...
