ArticleGenes to cells : devoted to molecular & cellular mechanisms2014
Quality control method for RNA-seq using single nucleotide polymorphism allele frequency.
Article in Genes to cells : devoted to molecular & cellular mechanisms, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed, 6 citations in OpenAlex.
- REDInet: a temporal convolutional network-based classifier for A-to-I RNA editing detection harnessing million known events.Briefings in bioinformatics · 2025Article
- Public Response to Scientific Misconduct: Assessing Changes in Public Sentiment Toward the Stimulus-Triggered Acquisition of Pluripotency (STAP) Cell Case via Twitter.JMIR public health and surveillance · 2017Article
- Article
- The Acid Test for Biological Science: STAP Cells, Trust, and Replication.Science and engineering ethics · 2016Article
- STAP cells are derived from ES cells.Nature · 2015Article
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Authors and funding
1 author at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
RNA sequencing (RNA-seq) provides information not only about the level of expression of individual genes but also about genomic sequences of host cells. When we use transcriptome data with whole-genome single nucleotide polymorphism (SNP) variant information, the allele frequency can show the genetic composition of the cell population and/or chromosomal aberrations. Here, I show how SNPs in mRNAs can be used to evaluate RNA-seq experiments by focusing on RNA-seq data based on a recently retracted paper on stimulus-triggered acquisition of pluripotency (STAP) cells. The analysis indicated that different types of cells and chromosomal abnormalities might have been erroneously included in the dataset. This re-evaluation showed that observing allele frequencies could help in assessing the quality of samples during a study and with retrospective evaluation of experimental quality.
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