GEO DataSets

(Submitter supplied) Abstract: The cellular and molecular dynamics of multiple sclerosis (MS) lesion development and repair cannot be inferred through study of postmortem tissue harvested decades after lesion onset. Employing MRI-informed spatiotemporal RNA profiling and experimental autoimmune encephalitis (EAE) in the common marmoset — a faithful model for these processes — we identified five microenvironmental groups pertinent to neural function, immune and glial responses, tissue destruction and repair, and regulatory networks at brain borders during lesion evolution. more...

Organism:

Callithrix jacchus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28240

26 Samples

Download data: RDATA

(Submitter supplied) Abstract: The cellular and molecular dynamics of multiple sclerosis (MS) lesion development and repair cannot be inferred through study of postmortem tissue harvested decades after lesion onset. Employing MRI-informed spatiotemporal RNA profiling and experimental autoimmune encephalitis (EAE) in the common marmoset — a faithful model for these processes — we identified five microenvironmental groups pertinent to neural function, immune and glial responses, tissue destruction and repair, and regulatory networks at brain borders during lesion evolution. more...

Organism:

Callithrix jacchus

Type:

Other

Platform:

GPL28240

16 Samples

Download data: H5, PNG, RDATA

(Submitter supplied) Background: Inhalation anesthetics may trigger the hypothalamic–pituitary–adrenal (HPA) axis. FK-506 binding protein (FKBP5) is a critical factor that regulates the HPA axis and is associated with perioperative neurocognitive impairment. However, it is unclear how inhalation anesthetics affects the expression of FKBP5 in different neural cells in the brain. Methods: We used single-nucleus RNA sequencing to characterize hippocampal transcriptome profiles in the brains of aged marmosets and mice after sevoflurane anesthesia. more...

Organism:

Callithrix jacchus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28240

6 Samples

Download data: MTX, TSV

(Submitter supplied) In primates, high-acuity vision is mediated by the fovea, a small specialized central region of the retina. The fovea, unique to the anthropoid lineage among mammals, undergoes notable neuronal morphological changes during postnatal maturation. However, the degree of cellular similarity across anthropoid foveas and the molecular underpinnings of foveal maturation remain unclear. Here, we used high throughput single cell RNA sequencing (scRNA-seq) to profile retinal cells of the common marmoset (Callithrix jacchus), an early divergent in anthropoid evolution from humans, apes, and macaques. more...

Organism:

Callithrix jacchus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL28240 GPL21580

24 Samples

Download data: BED, MTX, TSV

(Submitter supplied) Sequence divergence of cis-regulatory elements drives species-specific traits, but how this manifests in the evolution of the neocortex at the molecular and cellular level remains to be elucidated. We investigated the gene regulatory programs in the primary motor cortex of human, macaque, marmoset, and mouse with single-cell multiomics assays, generating gene expression, chromatin accessibility, DNA methylome, and chromosomal conformation profiles from a total of over 180,000 cells. more...

Organism:

Callithrix jacchus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL28240

5995 Samples

Download data: TSV

(Submitter supplied) Sequence divergence of cis-regulatory elements drives species-specific traits, but how this manifests in the evolution of neocortex at the molecular and cellular level remains to be elucidated. We investigated the gene regulatory programs in the primary motor cortex of human, macaque, marmoset, and mouse with single cell multiomics assays, generating gene expression, chromatin accessibility, DNA methylome and chromosomal conformation profiles from a total of over 180,000 cells. more...

Organism:

Mus musculus; Callithrix jacchus; Macaca mulatta; Homo sapiens

Type:

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

5 related Platforms

46 Samples

Download data: MTX, TSV

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

Organism:

Mustela putorius furo; Bos taurus; Anolis sagrei; Ictidomys tridecemlineatus; Homo sapiens; Sus scrofa domesticus; Rhabdomys pumilio; Danio rerio; Didelphis marsupialis; Peromyscus maniculatus; Tupaia chinensis; Callithrix jacchus; Ovis aries

Type:

Expression profiling by high throughput sequencing

13 related Platforms

118 Samples

Download data

(Submitter supplied) The basic plan of the retina is conserved across vertebrates, yet species differ profoundly in their visual needs (Baden et al., 2020). One might expect that retinal cell types evolved to accommodate these varied needs, but this has not been systematically studied. Here, we generated and integrated single-cell transcriptomic atlases of the retina from 17 species: humans, two non-human primates, four rodents, three ungulates, opossum, ferret, tree shrew, a teleost fish, a bird, a reptile and a lamprey. more...

Organism:

Callithrix jacchus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28240

8 Samples

Download data: CSV

(Submitter supplied) We sought to define and compare the diversity of cells across many brain areas, including various white matter (WM) regions, the volume and complexity of which is limited in mouse brain. We employed magnetic resonance (MR) image-guided sampling and snRNA-seq to survey the transcriptome at cellular resolution. Tissue types included WM (frontal, parietal, temporal), corpus callosum (anterior, posterior), optic tract, cerebral cortex (frontal, parietal, temporal, occipital, cingulate), caudate, hippocampus, lateral geniculate nucleus, cerebellum, thalamus, midbrain, pons, and cervical spinal cord. more...

Organism:

Callithrix jacchus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL28240 GPL26566 GPL18020

42 Samples

Download data: CSV, RDATA

(Submitter supplied) Adeno-associated virus (AAV)-mediated gene therapies are rapidly advancing to the clinic, and AAV engineering has resulted in vectors with increased ability to deliver therapeutic genes. Although the choice of vector is critical, quantitative comparison of AAVs, especially in large animals, remains challenging. Here, we developed an efficient single-cell AAV engineering pipeline (scAAVengr) to simultaneously quantify and rank efficiency of competing AAV vectors across all cell types in the same animal. more...

Organism:

Macaca fascicularis; Callithrix jacchus; Mus musculus

Type:

Expression profiling by high throughput sequencing

5 related Platforms

147 Samples

Download data: CSV, MTX, TSV, TXT

(Submitter supplied) Illustrating the cellular architecture of the mammalian brain is critical to understanding its diverse functions and complex animal behaviors. Single nucleus methylation sequencing was applied to M1 regions of human and mouse brains. we identified distinct cell clusters and formed them in a hierarchical taxonomy. These clusters include known primary brain cell types and possible sub-types. We use these data to identify the epigenomic characteristics and to define specific regulatory elements for each cell cluster.

Organism:

Callithrix jacchus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL28240

3043 Samples

Download data: TSV

(Submitter supplied) Illustrating the cellular architecture of the mammalian brain is critical to understanding its diverse functions and complex animal behaviors. Single nucleus methylation sequencing was applied to M1 regions of human and mouse brains. we identified distinct cell clusters and formed them in a hierarchical taxonomy. These clusters include known primary brain cell types and possible sub-types. We use these data to identify the epigenomic characteristics and to define specific regulatory elements for each cell cluster.

Organism:

Callithrix jacchus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL28240

3047 Samples

Download data: TSV

(Submitter supplied) We report single-nucleus transcriptomes from brain regions in 5 species: mice: Frontal Cortex, V1, Hippocampus, Striatum; common marmoset: 7 neocortical regions, Hippocampus, Striatum (Nucleus Accumbens, Caudate, Putamen); rhesus macaque: Prefrontal Cortex, V1; human: Prefrontal Cortex, V1, Striatum (Caudate); ferret: Prefrontal Cortex, V1, Striatum

Organism:

Callithrix jacchus; Macaca mulatta; Homo sapiens; Mustela putorius furo; Mus musculus

Type:

Expression profiling by high throughput sequencing

8 related Platforms

123 Samples

Download data: TXT