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Tissue-specific transcriptome sequencing analysis expands the non-human primate reference transcriptome resource (NHPRTR).

Peng X, Thierry-Mieg J, Thierry-Mieg D, Nishida A, Pipes L, Bozinoski M, Thomas MJ, Kelly S, Weiss JM, Raveendran M, Muzny D, Gibbs RA, Rogers J, Schroth GP, Katze MG, Mason CE - Nucleic Acids Res. (2014)

Bottom Line: The sequence quality is such that 88% of the reads align to human reference sequences, allowing us to compute the full list of expression abundance across all tissues for each species, using the reads mapped to human genes.This update also includes improved transcript annotations derived from RNA-seq data for rhesus and cynomolgus macaques, two of the most commonly used NHP models and additional RNA-seq data compiled from related projects.Together, these comprehensive reference transcriptomes from multiple primates serve as a valuable community resource for genome annotation, gene dynamics and comparative functional analysis.

View Article: PubMed Central - PubMed

Affiliation: Department of Microbiology, University of Washington, Seattle, WA 98109, USA Washington National Primate Research Center, Seattle, WA 98109, USA.

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Related in: MedlinePlus

Examples of genes showing conserved tissue-specific patterns across NHPs. On the heatmap, columns are AceView human gene symbols and rows are individual tissue samples. Same tissues from different species were grouped together as indicated by the color bands and labels on the right side of the heatmap. The color on the heatmap indicates the relative gene expression abundance in individual tissue samples. The relative expression abundance was calculated as log 2 transformed normalized sFPKM subtracted by the median of log 2 transformed normalized sFPKMs across all tissue samples for the same gene, therefore a unit of 1 is equal to a 2-fold increase in abundance in a tissue compared to the median of all samples from the same tissue.
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Figure 3: Examples of genes showing conserved tissue-specific patterns across NHPs. On the heatmap, columns are AceView human gene symbols and rows are individual tissue samples. Same tissues from different species were grouped together as indicated by the color bands and labels on the right side of the heatmap. The color on the heatmap indicates the relative gene expression abundance in individual tissue samples. The relative expression abundance was calculated as log 2 transformed normalized sFPKM subtracted by the median of log 2 transformed normalized sFPKMs across all tissue samples for the same gene, therefore a unit of 1 is equal to a 2-fold increase in abundance in a tissue compared to the median of all samples from the same tissue.

Mentions: The species assignment of each library was verified by analyzing over 5 million positions which appear as homozygous variant relative to human in at least one species. The analysis was facilitated by the fact that in most cases, all tissues in a species were coming from a single individual. We observed that each library was overwhelmingly sharing its homozygous SNPs only with the other libraries of the same species (average 99.987% identical SNPs, range: 99.56 to 100.00%). Therefore, all species and subspecies are consistently annotated. The correct assignment of tissues was verified using the covariance analysis of the expression patterns provided by the Magic pipeline (Supplementary Methods). Examples of tissue-specific genes are shown in FigureĀ 3.


Tissue-specific transcriptome sequencing analysis expands the non-human primate reference transcriptome resource (NHPRTR).

Peng X, Thierry-Mieg J, Thierry-Mieg D, Nishida A, Pipes L, Bozinoski M, Thomas MJ, Kelly S, Weiss JM, Raveendran M, Muzny D, Gibbs RA, Rogers J, Schroth GP, Katze MG, Mason CE - Nucleic Acids Res. (2014)

Examples of genes showing conserved tissue-specific patterns across NHPs. On the heatmap, columns are AceView human gene symbols and rows are individual tissue samples. Same tissues from different species were grouped together as indicated by the color bands and labels on the right side of the heatmap. The color on the heatmap indicates the relative gene expression abundance in individual tissue samples. The relative expression abundance was calculated as log 2 transformed normalized sFPKM subtracted by the median of log 2 transformed normalized sFPKMs across all tissue samples for the same gene, therefore a unit of 1 is equal to a 2-fold increase in abundance in a tissue compared to the median of all samples from the same tissue.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4383927&req=5

Figure 3: Examples of genes showing conserved tissue-specific patterns across NHPs. On the heatmap, columns are AceView human gene symbols and rows are individual tissue samples. Same tissues from different species were grouped together as indicated by the color bands and labels on the right side of the heatmap. The color on the heatmap indicates the relative gene expression abundance in individual tissue samples. The relative expression abundance was calculated as log 2 transformed normalized sFPKM subtracted by the median of log 2 transformed normalized sFPKMs across all tissue samples for the same gene, therefore a unit of 1 is equal to a 2-fold increase in abundance in a tissue compared to the median of all samples from the same tissue.
Mentions: The species assignment of each library was verified by analyzing over 5 million positions which appear as homozygous variant relative to human in at least one species. The analysis was facilitated by the fact that in most cases, all tissues in a species were coming from a single individual. We observed that each library was overwhelmingly sharing its homozygous SNPs only with the other libraries of the same species (average 99.987% identical SNPs, range: 99.56 to 100.00%). Therefore, all species and subspecies are consistently annotated. The correct assignment of tissues was verified using the covariance analysis of the expression patterns provided by the Magic pipeline (Supplementary Methods). Examples of tissue-specific genes are shown in FigureĀ 3.

Bottom Line: The sequence quality is such that 88% of the reads align to human reference sequences, allowing us to compute the full list of expression abundance across all tissues for each species, using the reads mapped to human genes.This update also includes improved transcript annotations derived from RNA-seq data for rhesus and cynomolgus macaques, two of the most commonly used NHP models and additional RNA-seq data compiled from related projects.Together, these comprehensive reference transcriptomes from multiple primates serve as a valuable community resource for genome annotation, gene dynamics and comparative functional analysis.

View Article: PubMed Central - PubMed

Affiliation: Department of Microbiology, University of Washington, Seattle, WA 98109, USA Washington National Primate Research Center, Seattle, WA 98109, USA.

Show MeSH
Related in: MedlinePlus