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Items: 1 to 20 of 68

1.

Epigenetic landscape of Mammalian Brain M1 by Single Nucleus Methylation Sequencing [MM_M1_2]

(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
Series
Accession:
GSE146633
ID:
200146633
2.

Epigenetic landscape of Mammalian Brain M1 by Single Nucleus Methylation Sequencing [MM_M1]

(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
Series
Accession:
GSE146608
ID:
200146608
3.

Epigenetic landscape of Mammalian Brain M1 by Single Nucleus Methylation Sequencing [M1_2]

(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
Series
Accession:
GSE146561
ID:
200146561
4.

Epigenetic landscape of Mammalian Brain M1 by Single Nucleus Methylation Sequencing [M1_1]

(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
Series
Accession:
GSE146525
ID:
200146525
5.

Genetic and transcriptomic identification of sensory neuron types underlying chronic pain in primates

(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
Series
Accession:
GSE148238
ID:
200148238
6.

Single cell transcriptomics of primate sensory neurons identifies cell types associated with human chronic pain

(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
Series
Accession:
GSE165569
ID:
200165569
7.

Single cell transcriptomics of primate sensory neurons identifies cell types associated with chronic pain [Wafergen]

(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
Series
Accession:
GSE165566
ID:
200165566
8.

Single cell transcriptomics of primate sensory neurons identifies cell types associated with chronic pain [SmartSeq2]

(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
Series
Accession:
GSE165553
ID:
200165553
9.

A method for spatially resolved tissue transcriptomics applied to the mouse and lizard P. vitticeps brains

(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
Series
Accession:
GSE152989
ID:
200152989
10.

Study of mechanisms by which Liver X Receptors regulate mouse midbrain dopaminergic neuron development

(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
Series
Accession:
GSE66197
ID:
200066197
11.

RNA-seq on mouse E11.5 ventral midbrain neurosphere cultures treated with the LXR agonist GW3965 and the GSK3beta inhibitor CT99021

(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
Series
Accession:
GSE66160
ID:
200066160
12.

ChIP-Seq for LXR in the mouse substantia nigra midbrain dopaminergic cell line SN4741 treated with the synthetic LXR ligand GW3965 for 1.5 hours

(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
Series
Accession:
GSE66118
ID:
200066118
13.

Multi-omic profiling of single nuclei uncovers regulatory diversity of brain cell types and diseases

(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
Series
Accession:
GSE140493
ID:
200140493
14.

A cell fitness selection model for neuronal survival during development

(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
Series
Accession:
GSE135181
ID:
200135181
15.

Simultaneous profiling of 3D genome structure and DNA methylation in single human cells

(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
16.

RNA-seq data of PatchSeq dataset from Pvalb-Cre positive interneurons in the mouse hippocamus CA1 region

(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
Series
Accession:
GSE130950
ID:
200130950
17.

Single cell data of microglia and perivascular macrophages identified from a single cell RNAseq analysis of mouse brain tissue.

(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
Series
Accession:
GSE120629
ID:
200120629
18.

Molecular analysis of the midbrain dopaminergic niche during neurogenesis

(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
Series
Accession:
GSE117394
ID:
200117394
19.

Single cell RNA-seq of the human long-term self-renewing neuroepithelial-like stem cell line SAI2

(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
Series
Accession:
GSE114670
ID:
200114670
20.

RNA-seq of miR-183 knockout mouse dorsal root ganglia

(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
Series
Accession:
GSE110714
ID:
200110714
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