title: Normalization of human RNA-seq experiments using chimpanzee RNA as a spike-in standard.
abstract: Normalization of human RNA-seq experiments employing chimpanzee RNA as a spike-in standard is reported. Human and chimpanzee RNAs exhibit single nucleotide variations (SNVs) in average 210-bp intervals. Spike-in chimpanzee RNA would behave the same as the human counterparts during the whole NGS procedures owing to the high sequence similarity. After discrimination of species origins of the NGS reads based on SNVs, the chimpanzee reads were used to read-by-read normalize biases and variations of human reads. By this approach, as many as 10,119 transcripts were simultaneously normalized for the entire NGS procedures leading to accurate and reproducible quantification of differential gene expression. In addition, incomparable data sets from different in-process degradations or from different library preparation methods were made well comparable by the normalization. Based on these results, we expect that the normalization approaches using near neighbor genomes as internal standards could be employed as a standard protocol, which will improve both accuracy and comparability of NGS results across different sample batches, laboratories and NGS platforms.
authors.affiliation: Center for Bioanalysis, Korea Research Institute of Standards and Science (KRISS), Korea.|Bioanalytical Science, University of Science and Technology (UST), Korea.
authors.forename: Hannah
authors.initials: H
authors.lastname: Yu
authors.affiliation: Department of Life Science, Chung-Ang University, Korea.
authors.forename: Yoonsoo
authors.initials: Y
authors.lastname: Hahn
authors.affiliation: Center for Bioanalysis, Korea Research Institute of Standards and Science (KRISS), Korea.|Bioanalytical Science, University of Science and Technology (UST), Korea.
authors.forename: Sang-Ryoul
authors.initials: SR
authors.lastname: Park
authors.affiliation: Medical Research Division, Korea Institute of Oriental Medicine (KIOM), Korea.
authors.forename: Sun-Ku
authors.initials: SK
authors.lastname: Chung
authors.affiliation: Medical Research Division, Korea Institute of Oriental Medicine (KIOM), Korea.
authors.forename: Sangkyun
authors.initials: S
authors.lastname: Jeong
authors.affiliation: Center for Bioanalysis, Korea Research Institute of Standards and Science (KRISS), Korea.|Bioanalytical Science, University of Science and Technology (UST), Korea.
authors.forename: Inchul
authors.initials: I
authors.lastname: Yang
mesh_terms: D000818:Animals; D002460:Cell Line; D030541:Databases, Genetic; D015870:Gene Expression; D015723:Gene Library; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D002679:Pan troglodytes / Q000235:genetics; D020641:Polymorphism, Single Nucleotide; D012313:RNA / Q000737:chemistry / Q000378:metabolism* / Q000592:standards; D017423:Sequence Analysis, RNA / Q000592:standards
chemical_list: D012313:RNA