GEO DataSets

(Submitter supplied) Saponin-based vaccine adjuvants are potent in preclinical animal models and humans, but their mechanisms of action remain poorly understood. Using a stabilized HIV envelope trimer as a model immunogen, we carried out studies in non-human primates (NHPs), comparing the most common clinical adjuvant alum and Saponin/MPLA Nanoparticles (SMNP), a novel ISCOMs-like adjuvant. SMNP elicited substantially stronger humoral immune responses than alum and induced strong type I interferon transcriptional signatures, expansion of innate immune cells, and increased antigen presenting cell activation in LNs. more...

Organism:

Macaca mulatta

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27943

7 Samples

Download data: MTX, RDS, TSV

(Submitter supplied) The cellular and genetic mechanism underlying the human-specific features of cortex development remains unclear. We generated a cell-type resolved atlas of transcriptome and chromatin accessibility of the developing macaque and mouse prefrontal cortex, and conducted evolutionary analyses with the published complementary human data. The cortex cell type composition shows an overall conservation across species. more...

Organism:

Macaca mulatta; Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:

GPL27943 GPL24247

33 Samples

Download data: BED, MTX, TXT

(Submitter supplied) Chikungunya virus (CHIKV) is a mosquito-borne alphavirus that has emerged as a significant public health concern due to its ability to cause severe arthralgia and occasionally fatal cases. The virus has been shown to infect a wide range of tissues, including the heart, liver, spleen, lungs, kidneys, and brain, leading to a spectrum of clinical manifestations.This study aims to investigate the impact of CHIKV infection on the transcriptome of various organs in rhesus monkeys and mice, providing insights into the molecular mechanisms underlying the pathogenesis of CHIKV in different host species.The transcriptome analysis revealed significant alterations in gene expression across the infected tissues in both species.

Organism:

Macaca mulatta; Mus musculus

Type:

Non-coding RNA profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:

GPL33913 GPL28330

72 Samples

Download data: XLS

(Submitter supplied) Authorization of the Matrix-M-adjuvanted R21 vaccine by three countries and its subsequent endorsement by the World Health Organization (WHO) for malaria prevention in children is a milestone in the fight against malaria. Yet, to meet the unprecedented demand for malarial vaccines, there is a pressing need for additional adjuvants that induce robust and durable vaccine-induced immunity. Here, we performed a comparative assessment of three clinically relevant adjuvants (an alum formulation of the TLR7/8 agonist 3M-052 (3M-052+Alum), the TLR4 agonist GLA-LSQ (GLA in liposome QS-21 formulation), and Matrix-M, the currently approved adjuvant for R21) for their capacity to induce durable immune responses to the R21 malaria vaccine in non-human primates. more...

Organism:

Macaca mulatta

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32224

256 Samples

Download data: TXT

(Submitter supplied) We thus isolated Anterior cingulate cortex (ACC) and Retro splenial cortex (RSC) from rhesus macaques and mice and performed single-cell RNA-sequencing analysis.The scRNA-Seq libraries were generated using the 10X Genomics Chromium Controller Instrument and Chromium Single Cell 3’ V2 Reagent Kits (10X Genomics, Pleasanton, USA).

Organism:

Mus musculus; Macaca mulatta

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL27943 GPL24247

11 Samples

Download data: MTX, TSV

(Submitter supplied) HIV cure efforts are increasingly focused on harnessing CD8 T cell functions; however, a deeper understanding of CD8 T cells promoting HIV control is necessary to properly inform therapeutic approaches. Here, we identified a novel TOX-expressing CD8 T cell population associated with control of SIV infection in lymphoid tissue of rhesus macaques defined as an antigen-responsive TCF1+ CD39+ subset expressing high levels of TOX and inhibitory receptors but lower levels of canonical cytolytic molecules such as granzyme B, granzyme A, and perforin. more...

Organism:

Macaca mulatta

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27943

5 Samples

Download data: H5

(Submitter supplied) In this study, the efficiency of four RNA extraction methods was compared on 23 FFPE cardiac tissue specimens. The Qiagen AllPrep DNA/RNA FFPE kit (Method QP), Qiagen AllPrep DNA/RNA FFPE kit, with protocol modification on the ethanol wash step after deparaffinization (Method QE), CELLDATA RNAstorm 2.0 FFPE RNA Extraction kit (Method BP) and CELLDATA RNAstorm 2.0 FFPE RNA Extraction Kit with protocol modifications on the lysis step (Method BL). more...

Organism:

Macaca mulatta

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27943

16 Samples

Download data: XLSX

(Submitter supplied) Structural variation (SV) is a class of genetic variants involving long stretches of DNA and provides substantial innovations for adaptation and evolution. Investigation of SV profiles and turnover in nonhuman primates can help answer fundamental questions, such as what makes us uniquely human. Here, we present the high-resolution comparative 3D genome organizations of prefrontal cortex (PFC) of adult human and rhesus macaque. more...

Organism:

Macaca mulatta; Homo sapiens

Type:

Other

Platforms:

GPL24676 GPL27943

2 Samples

Download data: BED, BEDPE

(Submitter supplied) We thus isolated prefrontal cotex from rhesus macaques and performed m6A-Seq analysis.MeRIP libraries using eluted RNA were constructed using the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian User Manual according to the manufacturer’s instructions.

Organism:

Macaca mulatta

Type:

Other

Platform:

GPL27943

22 Samples

Download data: TXT

(Submitter supplied) Here we use RNAseq and ATACseq to study the transcriptomics and epigenetic landscape of longitudinally sampled naïve and memory CD4+ and CD8+ T cells in two species of non-human primates prior to SIV infection, during chronic SIV infection, and after administration of ARVs. We find that SIV infection leads to significant alteration to the transcriptomic profile of all T cell subsets that are only partially reversed by administration of ARVs. more...

Organism:

Macaca nemestrina; Macaca mulatta

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL27943 GPL33261

116 Samples

Download data: TXT

(Submitter supplied) Here we use RNAseq and ATACseq to study the transcriptomics and epigenetic landscape of longitudinally sampled naïve and memory CD4+ and CD8+ T cells in two species of non-human primates prior to SIV infection, during chronic SIV infection, and after administration of ARVs. We find that SIV infection leads to significant alteration to the transcriptomic profile of all T cell subsets that are only partially reversed by administration of ARVs. more...

Organism:

Macaca nemestrina; Macaca mulatta

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL33261 GPL27943

120 Samples

Download data: BW, NARROWPEAK

(Submitter supplied) Human immunodeficiency virus (HIV) is widely recognized for its striking impact on the immune system. Even though HIV is primarily known for the impairment of the peripheral CD4 T cells, its influence on the central nervous system (CNS) also cannot be neglected. The main immune constituents in the brain, microglia and macrophages, are the target for HIV in the brain, as well as for the simian immunodeficiency virus (SIV) in nonhuman primates. more...

Organism:

Macaca mulatta

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL27943 GPL29319

20 Samples

Download data: H5

(Submitter supplied) Natural killer-like B (NKB) cells are unique innate immune cells that express both natural killer (NK) and B cell markers. They act as first responders by secreting IL-18 upon infection, thus inducing the critical cascade of innate and adaptive immune cell infiltration and activation. However, limited research exists on the role of NKB cells in homeostasis, and infection in primates. Therefore, we investigated the signaling and trafficking proteome, in situ localization and transcriptome of NKB cells in comparison to conventionally defined NK and B cells. more...

Organism:

Macaca mulatta

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27943

314 Samples

Download data: TXT

(Submitter supplied) Non-human primate (NHP)-based model systems are highly relevant for biomedical research. However, only few NHP cell lines are available and the generation of additional cell lines is an urgent need to help in the refinement and replacement of these models. Using lentiviral transduction of c-Fos, we established cell lines from the brain of rhesus macaques (Macaca mulatta). Transcriptome analysis revealed that these cell lines are closely related to astrocytes, which was confirmed by Western blot detecting expression of the astrocyte marker glial fibrillary acidic protein (GFAP). more...

Organism:

Macaca mulatta

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23949

4 Samples

Download data: CSV, TXT

(Submitter supplied) Alcohol use disorder is marked by disrupted behavioral and emotional states which can persist into abstinence. The enduring synaptic alterations that remain despite the absence of alcohol are of interest for interventions to prevent relapse. 28 male rhesus macaques underwent over 20 months of alcohol drinking interspersed with three 30-day forced abstinence periods. After the last abstinence period, we paired ex vivo voltammetry in nucleus accumbens slices with RNA-sequencing of the ventral tegmental area. more...

Organism:

Macaca mulatta

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27943

28 Samples

Download data: CSV, XLSX

(Submitter supplied) Glaucoma leads to vision loss due to retinal ganglion cell death. Astrocyte reactivity contributes to neurodegeneration. Our recent study found that lipoxin B4 (LXB4), produced by retinal astrocytes, has direct neuroprotective actions on retinal ganglion cells. In this study, we aimed to investigate how the autacoid LXB4 influences astrocyte reactivity in the retina under inflammatory cytokine-induced activation and ocular hypertension conditions. more...

Organism:

Macaca mulatta

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27943

2 Samples

Download data: CSV

(Submitter supplied) Theories of amygdala function are central to our understanding of psychiatric and neurodevelopmental disorders. However, our limited knowledge of the molecular and cellular composition of the amygdala impedes translational research aimed at developing new treatments and interventions. Here, we use single-nucleus RNA-sequencing from multiple amygdala subnuclei in both humans (n=3, Male) and rhesus macaques (n=3, Male) to begin to bridge the gap between preclinical rodent models and human disorders. more...

Organism:

Macaca mulatta; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32794

1 Sample

Download data: H5AD, XLSX

(Submitter supplied) There is growing appreciation for the emergence of CARneg bystander T cells after CAR-T cell infusion. However, their phenotypic and transcriptomic hallmarks and mechanisms of activation remain uncertain. We performed single-cell RNA-Seq (scRNA-Seq) on non-human primate (NHP) and patient-derived T cells to interrogate CARneg T cells following B cell targeted CAR-T cell therapy. In a NHP model, we observed a distinct population of activated CD8+ CARneg T cells emerging during CAR-T cell expansion. more...

Organism:

Macaca mulatta

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27943

35 Samples

Download data: HDF5, PT

(Submitter supplied) The hippocampus is especially susceptible to age-associated neuronal pathologies, and there is concern that the age-associated rise in cortisol secretion from the adrenal gland may contribute to their etiology. Furthermore, because 11β-hydroxysteroid dehydrogenase type 1 (HSD11B1) catalyzes the reduction of cortisone to the active hormone cortisol, it is plausible that an increase in the expression of this enzyme enhances the deleterious impact of cortisol in the hippocampus and contributes to the neuronal pathologies that underlie cognitive decline in the elderly. more...

Organism:

Macaca mulatta

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27943

28 Samples

Download data: CSV

(Submitter supplied) We performed spatial transcriptomics using Nanostring's DSP platform on Rhesus Macaque Hippocampal Brain sections obtained from one uninfected control and one chronically infected with SIVCL757. Our goals were to (1) determine which differentially expressed genes (DGEs) could be attributed to SIV infection in the rhesus hippocampus, (2) determine if spatial transcriptomics could serve as a tool to identify leukocyte infiltrates in the SIV infected brain and (3) examine localization of leukocytes at homeostatasis and chronic SIV infection

Organism:

Macaca mulatta

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27943

48 Samples

Download data: DCC