ArticlePloS one2017
Optimized approach for Ion Proton RNA sequencing reveals details of RNA splicing and editing features of the transcriptome.
Article in PloS one, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
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- Comparative transcriptomics of salivary basal cell adenoma and adenocarcinoma sustain linear neoplastic evolution and intertumor heterogeneity: classification and biological implications.The Journal of pathology · 2025Article
- Deep neural network based tissue deconvolution of circulating tumor cell RNA.Journal of translational medicine · 2023Article
- Targeting Translation and the Cell Cycle Inversely Affects CTC Metabolism but Not Metastasis.Cancers · 2023Article
- The immune response to a fungus in pancreatic cancer samples.bioRxiv : the preprint server for biology · 2023Article
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- Humanized Patient-derived Xenograft Models of Disseminated Ovarian Cancer Recapitulate Key Aspects of the Tumor Immune Environment within the Peritoneal Cavity.Cancer research communications · 2023Article
- The inflammatory response of human pancreatic cancer samples compared to normal controls.PloS one · 2023Article
- The RPL/RPS gene signature of melanoma CTCs associates with brain metastasis.Cancer research communications · 2022Article
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- Heterogeneity of Circulating Tumor Cell Neoplastic Subpopulations Outlined by Single-Cell Transcriptomics.Cancers · 2021Article
- Transcriptomic changes due to early, chronic intermittent alcohol exposure during forebrain development implicate WNT signaling, cell-type specification, and cortical regionalization as primary determinants of fetal alcohol syndrome.Alcoholism, clinical and experimental research · 2021Article
- Oncogenic Orphan Nuclear Receptor NR4A3 Interacts and Cooperates with MYB in Acinic Cell Carcinoma.Cancers · 2020Article
- Tetraspanin CD82 drives acute myeloid leukemia chemoresistance by modulating protein kinase C alpha and β1 integrin activation.Oncogene · 2020Article
- MYB - A regulatory factor in hematopoiesis.Gene · 2018Review
- Transcriptomes define distinct subgroups of salivary gland adenoid cystic carcinoma with different driver mutations and outcomes.Oncotarget · 2018Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
RNA-sequencing (RNA-seq) has become the standard method for unbiased analysis of gene expression but also provides access to more complex transcriptome features, including alternative RNA splicing, RNA editing, and even detection of fusion transcripts formed through chromosomal translocations. However, differences in library methods can adversely affect the ability to recover these different types of transcriptome data. For example, some methods have bias for one end of transcripts or rely on low-efficiency steps that limit the complexity of the resulting library, making detection of rare transcripts less likely. We tested several commonly used methods of RNA-seq library preparation and found vast differences in the detection of advanced transcriptome features, such as alternatively spliced isoforms and RNA editing sites. By comparing several different protocols available for the Ion Proton sequencer and by utilizing detailed bioinformatics analysis tools, we were able to develop an optimized random primer based RNA-seq technique that is reliable at uncovering rare transcript isoforms and RNA editing features, as well as fusion reads from oncogenic chromosome rearrangements. The combination of optimized libraries and rapid Ion Proton sequencing provides a powerful platform for the transcriptome analysis of research and clinical samples.
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