About

About NHPSTA

Non-Human Primate Seasonal Transcriptome Atlas (NHPSTA) is a database which provides the seasonal transcriptomes of 80 tissues collected every 2 months from one male and one female rhesus macaques (Macaca mulatta). Two modes of data exploration are included to: (1) compare the seasonal expression profiles of numerous genes of interest in a specific tissue type between sexes and (2) provide the seasonal transcriptomes for a specific gene across all tissue types.

Sample information

Adult rhesus macaques were reared in an open enclosure with natural light and temperature at the Center for the Evolutionary Origins of Human Behavior, Kyoto University, Inuyama, Japan. Two meals were provided daily at the estimated ad libitum levels and water was always available ad libitum. A total of 80 tissues, including 30 brain regions and 50 peripheral tissues, were collected from one male and one female every 2 months from October 2019 to August 2020 at around 15:00 (JST). Total RNA was then extracted using the Qiagen RNeasy Plus Universal Mini Kit.

Data generation and analysis

3' RNA-Seq libraries were prepared in accordance with the Lasy-Seq v1.1 protocol (https://sites.google.com/view/lasy-seq/). A maximum of 96 tagged libraries were mixed and sequenced with the Illumina HiSeq X Ten platform using pair-end sequencing. Mapping and quantification were performed with bowtie (v1.2.3) and RSEM (v1.3.3) using the Macaca mulatta reference genome (Genome assembly: Mmul_10). To improve the genome annotation, three annotation files (Ensembl: Macaca_mulatta.Mmul_10.192.gtf; NCBI: GCF_003339765.1_Mmul_10_genomic.gtf; GSE128537_assembly.rheMac10.gtf) were pooled to assemble a total of 54,213 genes. To perform seasonal expression profiling, each gene was plotted by fitting a cosine curve with the period of 365 days using the Nonlinear Least Squares (nls) function. Three parameters (amplitude, phase, and RS) that were obtained from the fitted curve, as well as the average expression level (mean) across six sampling time points, are displayed in each plot. The amplitude represents the difference between the maximum and minimum values of the seasonal oscillation; the phase represents the day at which the maximum value of the fitted curve is reached; and the coefficient of determination (R-squared, RS) was used to evaluate the goodness of the fit. Finally, Seasonally Oscillating Genes (SOGs) were extracted and shown in black with RS > 0.7 and amplitude > 1, equal to a 2-fold difference between the maximum and minimum expressions.

How to cite

Please cite the original publication:
Junfeng Chen, Kousuke Okimura, Liang Ren, Yusuke Nakane, Tomoya Nakayama, Yang Chen, Kai Fukawa, Soutarou Sugiyama, Takayoshi Natsume, Naoko Suda-Hashimoto, Mayumi Morimoto, Takako Miyabe-Nishiwaki, Takao Oishi, Yuma Katada, Manhui Zhang, Kohei Kobayashi, Shoko Matsumoto, Taiki Yamaguchi, Ying-Jey Guh, Issey Takahashi, Taeko Nishiwaki-Ohkawa, Daiki X. Sato, Yoshiharu Murata, Kenta Sumiyama, Atsushi J. Nagano, Hiroo Imai & Takashi Yoshimura
Non-human primate seasonal transcriptome atlas reveals seasonal changes in physiology and diseases.
Nature Communications (2025)
https://doi.org/10.1038/s41467-025-57994-1