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

Abstract

The non-human primate reference transcriptome resource (NHPRTR, available online at http://nhprtr.org/) aims to generate comprehensive RNA-seq data from a wide variety of non-human primates (NHPs), from lemurs to hominids. In the 2012 Phase I of the NHPRTR project, 19 billion fragments or 3.8 terabases of transcriptome sequences were collected from pools of ∼20 tissues in 15 species and subspecies. Here we describe a major expansion of NHPRTR by adding 10.1 billion fragments of tissue-specific RNA-seq data. For this effort, we selected 11 of the original 15 NHP species and subspecies and constructed total RNA libraries for the same ∼15 tissues in each. 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.

NeuN+ neuronal nuclei in non-human primate prefrontal cortex and subcortical white matter after clozapine exposure

“…Tissue from 12 of the 26 monkeys included in this study was available for RNA analysis (Table 1). Given that macaque tissues show very high degrees (92–95%) of transcriptome conservation in comparison to human(Peng et al, 2015), we wanted to study in our monkey specimens a set of transcripts subject to differential expression in human gray and white matter. To this end, we analyzed our RNAseq datasets from human postmortem gray and white matter homogenates(Dincer et al, 2015), and confirmed that the RBFOX3 and ABCA2 transcripts show strikingly different distribution.…”

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“…Paired-end reads with lengths of 100 nucleotides were generated. Raw data processing, read mapping, and gene expression quantification were done using the Magic-AceView analysis pipeline as described 27 . The Magic analysis tool is accessible at ftp://ftp.ncbi.nlm.nih.gov/repository/acedb/Software/Magic; AceView served as primary transcriptome reference (http://www.aceview.org).…”

Sooty mangabey genome sequence provides insight into AIDS resistance in a natural SIV host

“…The RNA-seq reads were pooled from 12 different tissues and were prepared by the standard mRNA-seq with the uracil DNA glycosylase protocol (Illumina kit Part RS-122-2303) and are publicly available from the Nonhuman Primate Reference Transcriptome Resource (NCBI SRA accession numbers SRX270666 and SRX270667) 27 . We performed a number of filtering steps to prepare threads for de novo assembly, which included removing adapters, filtering for quality, removing poly A/T tails and removing mtDNA and common mammalian rRNA 27,31 . After filtering, we used an input of 1,635,074,685 RNA-seq reads as the basis for the transcriptome assembly.…”