GEO DataSets

(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) 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:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL24676

3038 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:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL24676

3057 Samples

Download data: TSV

(Submitter supplied) Molecular characterization of the individual neuron types existing in the primate dorsal root ganglion and the relation to model organisms used for studying somatosensation and pain is critical for understanding the cellular origin of chronic pain and for translational aspects of biomedical research. However, molecular insights into the primate dorsal root ganglion are missing and a systematic comparison of strategies for somatosensation between the mouse and primates is lacking. more...

Organism:

Macaca mulatta

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19129

1845 Samples

Download data: CSV

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

Organism:

Macaca mulatta

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19129

7430 Samples

Download data

(Submitter supplied) Distinct types of dorsal root ganglion sensory neurons may have unique contributions to chronic pain. Identification of primate sensory neuron types is critical for understanding the cellular origin and heritability of chronic pain. However, molecular insights into the primate sensory neurons are missing. Here we classify non-human primate dorsal root ganglion sensory neurons based on their transcriptome and map human pain heritability to neuronal types. more...

Organism:

Macaca mulatta

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19129

4742 Samples

Download data: TAB

(Submitter supplied) Distinct types of dorsal root ganglion sensory neurons may have unique contributions to chronic pain. Identification of primate sensory neuron types is critical for understanding the cellular origin and heritability of chronic pain. However, molecular insights into the primate sensory neurons are missing. Here we classify non-human primate dorsal root ganglion sensory neurons based on their transcriptome and map human pain heritability to neuronal types. more...

Organism:

Macaca mulatta

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19129

2688 Samples

Download data: TAB

(Submitter supplied) We have developed an imaging-free framework to localize nucleic acids within a tissue by combining  a compressed sensing tissue-sampling strategy based on multi-angle-sectioning and an associated image reconstruction algorithm.  Initially, the tissue is cut into consecutive thin slices. Subsequently these are further sliced along an orthogonal plane at predefined orientations resulting in tissue strips that are subject to RNA sequencing. more...

Organism:

Mus musculus; Pogona vitticeps

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL28731 GPL13112

1200 Samples

Download data: TAB

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

Organism:

Mus musculus

Type:

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

Platform:

GPL13112

20 Samples

Download data: WIG

(Submitter supplied) We investigated mechanisms by which LXRs regulate midbrain dopaminergic neuron development. Using a systems biology approach, we found that LXR interacts with β-catenin and that LXR activation inhibits the activity of the Wnt/β-catenin pathway

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

12 Samples

Download data: TAB

(Submitter supplied) We investigated mechanisms by which LXRs regulate midbrain dopaminergic neuron development. Using a systems biology approach, we found that LXR interacts with β-catenin and that LXR activation inhibits the activity of the Wnt/β-catenin pathway

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13112

8 Samples

Download data: WIG

(Submitter supplied) Most existing single-cell techniques can only make one type of molecular measurements. Although computational approaches have been developed to integrate single-cell datasets, their efficacy still needs to be determined with reference to authentic single-cell multi-omic profiles. To address this challenge, we devised single-nucleus methylCytosine, Chromatin accessibility and Transcriptome sequencing (snmC2T-seq) and applied the approach to post-mortem human frontal cortex tissue. more...

Organism:

Homo sapiens

Type:

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

Platforms:

GPL16791 GPL20301 GPL24676

8494 Samples

Download data: CSV, HDF5, TSV

(Submitter supplied) Developmental cell death plays an important role in the construction of functional neural circuits. In vertebrate, the canonical view proposes a selection of the surviving neurons through stochastic competition for target-derived neurotrophic signals, implying an equal potential for neurons to compete. Here we show an alternative cell fitness selection of neurons that is defined by a specific neuronal heterogeneity code. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

2 Samples

Download data: TAB

(Submitter supplied) Dynamic 3D chromatin conformation is a critical mechanism for gene regulation during development and disease. Despite this, profiling of 3D genome structure from complex tissues with cell-type specific resolution remains challenging. Recent efforts have demonstrated that cell-type specific epigenomic features can be resolved in complex tissues using single-cell assays. However, it remains unclear whether single-cell Chromatin Conformation Capture (3C) or Hi-C profiles can effectively identify cell types and reconstruct cell-type specific chromatin conformation maps. more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing; Other

Platforms:

GPL20301 GPL24676

4238 Samples

Download data: TSV, TXT

(Submitter supplied) This study takes on the problem of bridging transcriptional data to neuronal phenotype and function by using publicly available datasets characterizing distinct neuronal populations based on gene expression, electrophysiology and morphology. In addition, a non-published PatchSeq dataset of Pvalb-cre positive cells in CA1 was used, which is the dataset submitted here. Taken together, these datasets were used to identify cross-cell type correlations between these data modalities. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Third-party reanalysis

Platform:

GPL17021

19 Samples

Download data: TXT

(Submitter supplied) Single cell sequencing of microglia and perivascular macrophages was performed on brain tissue from different brain regions to obtain single cell expression profiles dependent on celltype and regional location.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

425 Samples

Download data: CSV

(Submitter supplied) Midbrain dopaminergic (mDA) neurons degenerate in Parkinson's disease and are one of the main targets for cell replacement therapies. A comprehensive view of the signals and cell types contributing to mDA neurogenesis is not yet available. By analyzing the transcriptome of the mouse ventral midbrain at tissue and single-cell level during mDA neurogenesis we found that three recently identified radial glia types (Rgl 1-3) contribute to different key aspects of mDA neurogenesis. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

60 Samples

Download data: TSV

(Submitter supplied) The transcriptome of single long-term self-renewing neuroepithelial-like stem cells (LT-NES) was studied in order to establish a baseline for investigations into modules of synergistically active transcription factors that determine developmental cell subpopulations

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

288 Samples

Download data: TAB

(Submitter supplied) To identify the mechanism by which the miR-183 cluster works to cause change of the fate of early dorsal root ganglion progenitor cells, we compared RNA expression in E12.5 lumbar dorsal root ganglia from the miR conditional knockout mice to control mice

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11002

6 Samples

Download data: CSV