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Transcriptome software results show significant variation among different commercial pipelines
BackgroundWe have been documenting the biological responses to low levels of radiation (natural background) and very low level radiation (below...
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A transcriptome software comparison for the analyses of treatments expected to give subtle gene expression responses
BackgroundIn this comparative study we evaluate the performance of four software tools: DNAstar-D (DESeq2), DNAstar-E (edgeR), CLC Genomics 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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Sequencing of Transcriptome-Wide Poly(A) Tails by PAIso-seq
Poly(A) tails are added to most eukaryotic mRNA and have essential regulatory functions. However, due to its homopolymeric nature, the sequence...
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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-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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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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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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transXpress: a Snakemake pipeline for streamlined de novo transcriptome assembly and annotation
BackgroundRNA-seq followed by de novo transcriptome assembly has been a transformative technique in biological research of non-model organisms, but...
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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 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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Transcriptome analysis of reproductive tract tissues of male river prawn Macrobrachium americanum
BackgroundThe river prawn, Macrobrachium americanum (M. americanum), is one of the largest prawns of the genus in Latin America and is an...
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StringFix: an annotation-guided transcriptome assembler improves the recovery of amino acid sequences from RNA-Seq reads
BackgroundReconstruction of amino acid sequences from assembled transcriptome is of interest in personalized medicine, for example, to predict...
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What Is the Transcriptome and How It Is Evaluated
The concept of the transcriptome revolves around the complete set of transcripts present in a given cell type, tissue, or organ and encompasses both...
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Droplet-based transcriptome profiling of individual synapses
Synapses are crucial structures that mediate signal transmission between neurons in complex neural circuits and display considerable morphological...
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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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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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UNAGI: Yeast Transcriptome Reconstruction and Gene Discovery Using Nanopore Sequencing
Computational approaches are the main approaches used in genome annotation. However, accuracy is low. Untranslated regions are not identified,...
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Integrative temporal multi-omics reveals uncoupling of transcriptome and proteome during human T cell activation
Engagement of the T cell receptor (TCR) triggers molecular reprogramming leading to the acquisition of specialized effector functions by CD4 helper...
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GTax: improving de novo transcriptome assembly by removing foreign RNA contamination
The cost and complexity of generating a complete reference genome means that many organisms lack an annotated reference. An alternative is to use a...
