GEO DataSets

(Submitter supplied) Releated to the single nucleus RNA sequencing data displayed in Extended Data Figure 1

Organism:

Macaca mulatta; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL14954 GPL11154

28 Samples

Download data: MTX, TSV

(Submitter supplied) We conducted a comprehensive transcriptome analysis of whole blood from male and female nonhuman primates (rhesus macaque (Macaca mulatta)) that received upper thoracic radiation. A Varian CLINAC 21EX linear accelerator was used (6 MV Linear Accelerator (Linac)). Body Weight Range: 3.5 to 5 kg (at initial physical exam). Age Range: 3 to 5 years (at initial physical exam).

Organism:

Macaca mulatta

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14954

304 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Macaca mulatta; Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL13112 GPL11154 GPL14954

184 Samples

Download data

(Submitter supplied) We implemented transcriptomic analyses of blood from young and aged monkey

Organism:

Macaca mulatta

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14954

20 Samples

Download data: XLS

(Submitter supplied) To characterize the early immune responses against coronavirus infection, we infected rhesus macaques and hACE2 transgenic mice with SARS-CoV-2 and analyzed the transcriptome of infected and non-infected animals. We infected WT mice with IAV as a normal respiratory virus group. During analysis, we found that S100A8 was dramatically upregulated by SARS-CoV-2 and a mouse coronavirus (mouse hepatitis virus, MHV), but not by other tested viruses. more...

Organism:

Macaca mulatta; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL13112 GPL14954

44 Samples

Download data: XLSX

(Submitter supplied) Transposable elements (TE) account for more than 50% of human genome. It has been reported that some types of TEs are dynamically regulated in the reprogramming of human cell lines. However, it is largely unknown whether some TEs in Macaca mulatta are also regulated during the reprogramming of cell lines of monkey. Here, we systematically examined the transcriptional activities of TEs during the conversion of Macaca mulatta fibroblast cells to neuroepithelial stem cells (NESCs). more...

Organism:

Macaca mulatta

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14954

14 Samples

Download data: XLSX

(Submitter supplied) Elucidating the regulatory mechanisms of human brain evolution is essential to understanding human cognition and mental disorders. We generated multi-omics profiles and constructed a high-resolution map of 3D genome architecture of rhesus macaque during corticogenesis. By comparing the 3D genomes of human, macaque and mouse brains, we identified many human-specific chromatin structure changes, including 499 topologically associating domains (TADs) and 1,266 chromatin loops. more...

Organism:

Macaca mulatta

Type:

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

Platform:

GPL14954

18 Samples

Download data: BED, BEDPE, BW, HIC, NARROWPEAK, TXT

(Submitter supplied) Brain development is exceptionally delayed in humans compared to nonhuman primates (NHPs), a finding often termed neoteny. Signatures of neoteny, including a protracted proliferation of apical and basal progenitors as well as a delay in physiological activity of mature neurons, have been revealed in part through the use of induced pluripotent stem cell (iPSC) modeling of primate neurogenesis. IPSC modeling is particularly useful when examining the molecular drivers of a cellular phenotype such as gene transcription. more...

Organism:

Gorilla; Pan paniscus; Macaca mulatta; Pan troglodytes; Homo sapiens

Type:

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

10 related Platforms

79 Samples

Download data: BED, BEDGRAPH, TXT

(Submitter supplied) The advent of animal husbandry and hunting increased human exposure to zoonotic pathogens. To understand how a zoonotic disease influenced human evolution, we studied changes in human expression of anthrax toxin receptor 2 (ANTXR2), which encodes a cell surface protein necessary for Bacillus anthracis virulence toxins to cause anthrax disease. In immune cells, ANTXR2 was 8-fold down-regulated in all available human samples compared to non-human primates, indicating regulatory changes early in the evolution of modern humans. more...

Organism:

Macaca mulatta; Papio anubis

Type:

Other

Platforms:

GPL30489 GPL14954 GPL27943

12 Samples

Download data: HIC, SF, TXT

(Submitter supplied) We report the whole genome transcriptomic responses of ape species (human, common chimpanzee) and AAMs (rhesus macaque and olive baboon) to bacterial and viral stimulation. We find stark differences in the responsiveness of these groups, with apes mounting a markedly stronger early transcriptional response to both viral and bacterial stimulation, altering the transcription of ∼40% more genes than AAMs. more...

Organism:

Papio anubis; Macaca mulatta; Pan troglodytes; Homo sapiens

Type:

Expression profiling by high throughput sequencing

4 related Platforms

151 Samples

Download data: TXT

(Submitter supplied) We report the application of RNA sequencing technology for high-throughput profiling of RNA expression in monkey tissues. By obtaining over four billion bases of sequence of brain, liver and muscle from MCPH1 trasngenic monkey and two control monkeys. We find that brain tissue showed more differentially expressed genes compared with those in liver and muscle. Finally, we show that This result implies that the overexpressed huMCPH1 may have a global impact on multiple organs of the transgenic monkey, and it has the largest impact on the brain in terms of gene numbers. more...

Organism:

Macaca mulatta

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14954

63 Samples

Download data: TXT

(Submitter supplied) Purpose: Evaluated the transcriptional effects of an effective oral dosing of antental corticosteroids using betamethasone-phophate compared to the clinical treatment with the combination drug betamethasone-phosphate+betamethasone-acetate for fetal lung maturation. Methods: RNA-sequencing of the fetal hippocampus, liver and lung was done. Differential expression analysis was done using read counts. Results: There were no significant differences between oral Beta-P and the clinical treatment in the fetal hippocampus. Small differences were detected in the fetal lung associated with cellular proliferation and in the fetal liver. Conclusions: Oral betamethasone-phosphate is an effective oral treatment that does not cause toxic effect in the fetal brain despite the higher dose.

Organism:

Macaca mulatta

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14954

24 Samples

Download data: CSV

(Submitter supplied) MicroRNAs are small non-coding RNAs that are critical in post-transcriptional regulation. According to the latest miRBase (v22), there are 617 annotated pre-miRNAs in Macaca mulatta, which is much less than 1917 in human, although both of these two species are primates. To improve the annotation of miRNAs in Macaca mulatta, we generated 12 small RNA profiles from 8 tissues and perform comprehensive analysis of these profiles. more...

Organism:

Macaca mulatta

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL14954

12 Samples

Download data: TXT

(Submitter supplied) Ten diet-induced obese Rhesus macaques were treated with fibroblast growth factor 21 (FGF21) for 12 weeks, which resulted in an average of 18% weight loss. Tissue punch biopsies were taken from abdominal subcutaneous adipose tissue and gastrocnemius skeletal muscle pre-treatment, at the end of treatment, and after a 16 week washout period. Numerous genes were found to be differentially expressed between pre-treatment, post-treatment, and washout time points in adipose tissue; however, high amounts of inter-sample variation in muscle tissue gene expression levels obscured any differences between pre- and post-treatment in skeletal muscle.

Organism:

Macaca mulatta

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14954

51 Samples

Download data: CSV

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus; Macaca mulatta; Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

4 related Platforms

31 Samples

Download data: WIG

(Submitter supplied) Mechanisms by which the mammalian gametes encode epigenetic information that can be transmitted to the progeny are relatively unknown. We find that many sperm promoters in mouse sperm are occupied by phosphorylated forms of RNA polymerase II and the Mediator complex. Analysis of ATAC-seq data suggest that the same promoters are occupied by components of the transcription complex in GV and MII oocytes and preimplantation embryos. more...

Organism:

Mus musculus; Macaca mulatta; Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL13112 GPL11154 GPL14954

10 Samples

Download data: WIG

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Chlorocebus aethiops; Macaca mulatta

Type:

Expression profiling by high throughput sequencing

4 related Platforms

124 Samples

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(Submitter supplied) We devised a systems biology approach to investigate the early host response to high-dose rectal SIV transmission, by transcriptomic comparative analysis of a natural reservoir host SIV model species, African green monkeys (AGMs – Chlorocebus sabaeus, N=28) and a pathogenic model, rhesus macaques (RMs - Macaca mulatta, N=24).on rectal tissues for both AGMs and RMs.

Organism:

Chlorocebus aethiops; Macaca mulatta

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24584 GPL14954

79 Samples

Download data: TXT

(Submitter supplied) We compared a 5 week time course of cortical organoid differentiation across human, chimpanzee, orangutan, and rhesus using bulk RNAseq. In addition, single cell RNAseq was performed on a subset of time points from human cells in weeks 0, 1, 2, and 5.

Organism:

Pan troglodytes; Pongo abelii; Macaca mulatta; Homo sapiens

Type:

Expression profiling by high throughput sequencing

5 related Platforms

55 Samples

Download data: GTF, TAR, TSV, TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Macaca mulatta; Nomascus leucogenys

Type:

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

Platforms:

GPL14954 GPL25056 GPL25055

6 Samples

Download data: BED, BEDGRAPH