Conserved expression of lincRNA during human and macaque prefrontal cortex development and maturation
Ontology highlight
ABSTRACT:
ORGANISM(S): Macaca mulatta
SUBMITTER: Zhisong He
PROVIDER: E-GEOD-51264 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:The human brain has changed dramatically from other primate species, but the genetic and developmental mechanisms behind the differences remains unclear. Here we used single cell RNA sequencing based on 10X technology to explore temporal transcriptomic dynamics and cellular heterogeneity in cerebral organoids derived from human and non-human primates chimpanzee and rhesus macaque stem cells. Using cerebral organoids as a proxy of early brain development, we detect a delayed pace of human brain development relative to the other two primate species. Additional human-specific gene expression patterns resolved to different cell states through progenitors to neurons are also found. Our data provide a transcriptomic cell atlas of primate early brain development, and illustrate features that are unique to humans.
2019-10-04 | E-MTAB-8234 | biostudies-arrayexpress
Project description:We investigated molecular changes during human, chimpanzee, and rhesus macaque postnatal brain development at the transcriptome, proteome, and metabolome levels in two brain regions: the prefrontal cortex (PFC) that is involved in several human-specific cognitive processes, and the cerebellar cortex (CBC) that may be functionally more conserved. We find a nearly three-fold excess of human-specific gene expression changes in PFC compared to CBC. The most prominent human-specific mRNA expression pattern in the PFC is a developmental delay of approximately 5 years in the expression of genes associated with learning and memory, such as synaptic transmission and long-term potentiation. This pattern is supported by correlated changes in concentrations of proteins and the respective neurotransmitters and its magnitude is beyond the shift expected from the life-histories of the species. Mechanistically, it might be driven by change in timing of expression of four or more transcription factors. We speculate that delayed synaptic maturation in PFC may play a role in the emergence of human-specific cognitive abilities. Keywords: Age series Human, chimpanzee and rhesus macaque post-mortem brain samples from the superior frontal gyrus region of the prefrontal cortex were collected. The age ranges of the individuals in all three species covered the respective species' postnatal maturation period from infancy to old adulthood. RNA extracted from the dissected tissue was hybridized to Affymetrix® Human Gene 1.0 ST arrays. PFC samples.
2011-12-09 | E-GEOD-22521 | biostudies-arrayexpress
Project description:We investigated molecular changes during human, chimpanzee, and rhesus macaque postnatal brain development at the transcriptome, proteome, and metabolome levels in two brain regions: the prefrontal cortex (PFC) that is involved in several human-specific cognitive processes, and the cerebellar cortex (CBC) that may be functionally more conserved. We find a nearly three-fold excess of human-specific gene expression changes in PFC compared to CBC. The most prominent human-specific mRNA expression pattern in the PFC is a developmental delay of approximately 5 years in the expression of genes associated with learning and memory, such as synaptic transmission and long-term potentiation. This pattern is supported by correlated changes in concentrations of proteins and the respective neurotransmitters and its magnitude is beyond the shift expected from the life-histories of the species. Mechanistically, it might be driven by change in timing of expression of four or more transcription factors. We speculate that delayed synaptic maturation in PFC may play a role in the emergence of human-specific cognitive abilities. Keywords: Age series Human, chimpanzee and rhesus macaque post-mortem brain samples from the cerebellar cortex were collected. The age ranges of the individuals in all three species covered the respective species' postnatal maturation period from infancy to old adulthood. RNA extracted from the dissected tissue was hybridized to Affymetrix® Human Gene 1.0 ST arrays. CBC samples.
2011-12-09 | E-GEOD-22569 | biostudies-arrayexpress
Project description:This dataset was generated with the goal of comparative study of gene expression in three brain regions and two non-neural tissues of humans, chimpanzees, macaque monkeys and mice. Using this dataset, we performed studies of gene expression and gene splicing evolution across species and search of tissue-specific gene expression and splicing patterns. We also used the gene expression information of genes encoding metabolic enzymes in this dataset to support a larger comparative study of metabolome evolution in the same set of tissues and species. 120 tissue samples of prefrontal cortex (PFC), primary visual cortex (VC), cerebellar cortex (CBC), kidney and skeletal muscle of humans, chimpanzees, macaques and mice. The data accompanies a large set of metabolite measurements of the same tissue samples. Enzyme expression was used to validate metabolite measurement variation among species.
2014-05-30 | E-GEOD-49379 | biostudies-arrayexpress
Project description:We search for developmental changes specific to humans by examining gene expression profiles in the human, chimpanzee and rhesus macaque prefrontal and cerebellar cortex. In both brain regions, developmental patterns were more evolved in humans than in chimpanzees. To distinguish whether the human specific developmental pattern represent novel human-specific developmental patterns or a shift in the timing of the existing patterns, we measured mRNA expression patterns in macaque brains from prenatal to neonatal. Our results show that the major human-specific developmental patterns identified in the PFC reflects an extreme shift in timing of synaptic development. Rhesus macaque post-mortem brain samples from the superior frontal gyrus region of the prefrontal cortex were collected. Six fetal and six newborn samples were used. RNA extracted from the dissected tissue was hybridized to Affymetrix® Human Gene 1.0 ST arrays.
2012-02-02 | E-GEOD-29138 | biostudies-arrayexpress
Project description:Small RNA including microRNA (miRNA) and Piwi-interacting RNA (piRNA) play important roles in germline maintenance and maturation in wide variety of species. Relatively little however is known about role played by miRNA in male germline maturation in humans and closely related primate species. Here we focused on rhesus macaques as a model species closely related to humans to study small RNA expression in testis samples throughout postnatal development and maturation. We observe clear transition in miRNA and piRNA expression resulting in the overall increase of piRNA expression levels and corresponding decrease in miRNA expression. Unexpectedly, this transition takes place at approximately one year of age – far earlier then rhesus macaque sexual maturation occurring at 4-5 years of age. Notably, contradictory to the overall trend of expression decline, a group of 29 miRNA showed marked expression increase in macaque testis at approximately five years of age – the time interval associated with sexual maturation. Keywords: miRNA piRNA Age Series Rhesus macaque post-mortem testicle samples were collected. The age ranges of the indibiual in rhesus macaque covered the whole life span fom newborn to death.
2013-03-05 | E-GEOD-44820 | biostudies-arrayexpress
Project description:RNA-seq samples from 3 species across a differentiation from induced pluripotent stem cells to neural progenitor cells were generated to study gene expression evolution. Briefly, previously generated urinary stem cell derived iPSCs of 3 human (Homo sapiens) individuals (3 clones), 1 gorilla (Gorilla gorilla) individual and fibroblast derived cynomolgus macaque (Macaca fascicularis) iPSCs of 2 individuals (4 clones) (Geuder et al. 2021) were differentiated to neural progenitor cells via dual-SMAD inhibition as three-dimensional aggregation culture (Chambers et al. 2009; Ohnuki et al. 2014). Bulk RNA-seq libraries of iPSCs and NPCs were generated using prime-seq protocol (Janjic et al. 2022).
2023-11-23 | E-MTAB-13494 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE17757: Gene expression data from primate postnatal brain in prefrontal cortex: time course GSE18012: miRNA expression data from human postnatal brain in prefrontal cortex: time course GSE18013: miRNA expression data from rhesus macaque postnatal brain in prefrontal cortex: time course Refer to individual Series
2010-06-09 | E-GEOD-18069 | biostudies-arrayexpress
Project description:Gene expression changes determine functional differentiation during development and are associated with functional decline during aging. While developmental changes are tightly regulated, regulation of aging changes is not well established. To assess the regulatory basis of age-related changes and investigate the mechanism of regulatory transition between development and aging, we measured mRNA and microRNA expression patterns in brains (superior frontal gyrus) of humans and rhesus macaques over the entire speciesâ lifespan. We find that in both species, developmental and aging changes overlap in the course of lifetime with many changes found at the late age initiating in early childhood. Human post-mortem brain samples from the superior frontal gyrus region of the prefrontal cortex were collected. The age ranges of the indibiual in human covered its whole life span fom newborn to death. RNA extracted from the dissected tissue was hybridized to Affymetrix® Human Gene 1.0 ST arrays. Rhesus macaque post-mortem brain samples from the superior frontal gyrus region of the prefrontal cortex were collected. The age ranges of the indibiual in rhesus macaque covered the whole life span fom newborn to death. RNA extracted from the dissected tissue was hybridized to Affymetrix® Human Gene 1.0 ST arrays.
2010-06-24 | E-GEOD-17757 | biostudies-arrayexpress
Project description:We performed an evolutionary comparison of the binding of the TF CTCF in human, chimpanzee, gorilla, orang-utan, macaque, baboon and marmoset using lymphoblastoid cell lines (LCLs). We also probes YY1 binding in human, chimpanzee, orang-utan and baboon LCLs as well as human and mouse liver.
2013-11-20 | E-MTAB-1511 | biostudies-arrayexpress