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Transcriptome Analysis Using RNA-Seq [PDF]
, 2012 Transcriptome analysis by next-generation sequencing (RNA-seq) allows investigation of a transcriptome at unsurpassed resolution. One major benefit is that RNA-seq is independent of a priori knowledge on the sequence under investigation, thereby also allowing analysis of poorly characterized Plasmodium species.
Hoeijmakers, W.A.M. +2 more
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trumpet: transcriptome-guided quality assessment of m6A-seq data
BMC Bioinformatics, 2018 Background Methylated RNA immunoprecipitation sequencing (MeRIP-seq or m6A-seq) has been extensively used for profiling transcriptome-wide distribution of RNA N6-Methyl-Adnosine methylation.
Teng Zhang +3 more
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NBLDA: Negative Binomial Linear Discriminant Analysis for RNA-Seq Data
, 2015 RNA-sequencing (RNA-Seq) has become a powerful technology to characterize gene expression profiles because it is more accurate and comprehensive than microarrays. Although statistical methods that have been developed for microarray data can be applied to
Dong, Kai +3 more
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Systematic evaluation of spliced alignment programs for RNA-seq data [PDF]
, 2018 High-throughput RNA sequencing is an increasingly accessible method for studying gene structure and activity on a genome-wide scale. A critical step in RNA-seq data analysis is the alignment of partial transcript reads to a reference genome sequence.
Bertone, P +10 more
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RNA‐Seq for Bacterial Gene Expression [PDF]
Current Protocols in Nucleic Acid Chemistry, 2018 AbstractRNA sequencing (RNA‐seq) has become the preferred method for global quantification of bacterial gene expression. With the continued improvements in sequencing technology and data analysis tools, the most labor‐intensive and expensive part of an RNA‐seq experiment is the preparation of sequencing libraries, which is also essential for the ...
Poulsen, Line Dahl, Vinther, Jeppe
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Polymorphism identification and improved genome annotation of Brassica rapa through Deep RNA sequencing. [PDF]
, 2014 The mapping and functional analysis of quantitative traits in Brassica rapa can be greatly improved with the availability of physically positioned, gene-based genetic markers and accurate genome annotation.
Covington, Michael F +4 more
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Dissecting intratumoral myeloid cell plasticity by single cell RNA‐seq
Cancer Medicine, 2019 Tumor‐infiltrating myeloid cells are the most abundant leukocyte population within tumors. Molecular cues from the tumor microenvironment promote the differentiation of immature myeloid cells toward an immunosuppressive phenotype.
Qianqian Song +19 more
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Polyribosomal RNA-Seq reveals the decreased complexity and diversity of the Arabidopsis translatome.
PLoS ONE, 2015 Recent RNA-seq studies reveal that the transcriptomes in animals and plants are more complex than previously thought, leading to the inclusion of many more splice isoforms in annotated genomes. However, it is possible that a significant proportion of the
Xingtan Zhang +4 more
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Design, execution, and interpretation of plant RNA-seq analyses
Frontiers in Plant Science, 2023 Genomics has transformed our understanding of the genetic architecture of traits and the genetic variation present in plants. Here, we present a review of how RNA-seq can be performed to tackle research challenges addressed by plant sciences.
Racheal N. Upton +6 more
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An observation of circular RNAs in bacterial RNA-seq data [PDF]
, 2016 Circular RNAs (circRNAs) are a class of RNA with an important role in micro RNA (miRNA) regulation recently discovered in Human and various other eukaryotes as well as in archaea.
Aurell, Erik +3 more
core +1 more source