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295 results for “midbrain”
Spatial Transcriptomics data (GeoMx) of midbrain dopamine cells in control and PD subjects
<p>The repository includes Spatial Transcriptomic datasets generated by Nanostring GeoMx (Hu WTA) analysis of midbrain TH+ cells from Controls (n=10), Incidental Lewy Body Disease (n=10), early Parkinsons Disease (ePD,n=5) and late Parkinsons Disease (lPD,n=5). A total 348 Regions of Interest were analysed. The raw and processed counts and metadata are provided as an R Seurat object (geomx_edwards_thmask.rds). The scripts used for low level data processing are described in https://github.com/zchatt/ASAP-SpatialTranscriptomics/blob/main/geomx/lowlevel/README.md</p> <p>Tissue samples from pathologically confirmed asymptomatic stage I-II Lewy body disease, stage IV Lewy body PD (early-PD), stage VI Lewy body PD (late-PD)(Braak, Del Tredici et al. 2003) and controls without the neurological or neuropathological disease were obtained from the Sydney Brain Bank. The study was approved by the University of Sydney Human Research Ethics Committee (2021/845). All cases with PD were levodopa-responsive and fulfilled the UK Brain Bank Clinical Criteria for a diagnosis of clinical PD (Hughes, Ben-Shlomo et al. 1992) with no other neurodegenerative conditions. </p> <p>Cells were not extracted. Tissue sections were cut from FFPE blocks of post-mortem human midbrains at 6µm on a rotary microtome (HistoCore MULTICUT, Leica Biosystems) and mounted on Series 2 adhesive microscope slides (Trajan Scientific Medical, AU) for processing for spatial trranscriptomics. To remove the paraffin, slides were incubated in the oven at 60°C for 1hr and then submerged in HistoChoice Clearing Agent (Sigma-Aldrich, H2779) for 2x7mins, followed by rehydration in decreasing ethanol concentrations (100% ethanol for 2x3mins, 95% ethanol for 3mins, 70% ethanol for 3mins) and distilled H2O for 3mins. </p> <p>Tissue sections were immunohistochemically stained for tyrosine hydroxylase and Regions of Interest (ROIs) processed following Nanostring GeoMx® Digital Spatial Profiler using the manufacturer’s instructions. Libraries were sequenced on Illumina Novaseq 6000 platform using NovaSeq SP 100 cycle kit (XP workflow, 27-8-8-27).</p> <p>This research was funded in whole or in part by Aligning Science Across Parkinson’s (ASAP-020529) through the Michael J. Fox Foundation for Parkinson’s Research (MJFF). For the purpose of open access, the author has applied a CC BY 4.0 public copyright license to all Author Accepted Manuscripts arising from this submission.</p>
Spatial Transcriptomics data (GeoMx) of midbrain tissue in control and PD subjects
<p>he repository includes Spatial Transcriptomic datasets generated by Nanostring GeoMx (Hu WTA) analysis of midbrain unmasked (whole tissue) Regions of Interest from Controls (n=10), Incidental Lewy Body Disease (n=11), early Parkinsons Disease (ePD, n=5) and late Parkinsons Disease (lPD, n=6). A total 515 Regions of Interest were analysed. The raw and processed counts and metadata are provided as an R Seurat object (geomx_vila_unmask.rds). The scripts used for low level data processing are described in https://github.com/zchatt/ASAP-SpatialTranscriptomics/blob/main/geomx/lowlevel/README.md </p> <p>Tissue samples from pathologically confirmed asymptomatic stage I-II Lewy body disease, stage IV Lewy body PD (early-PD), stage VI Lewy body PD (late-PD)(Braak, Del Tredici et al. 2003) and controls without the neurological or neuropathological disease were obtained from the Sydney Brain Bank. The study was approved by the University of Sydney Human Research Ethics Committee (2021/845). All cases with PD were levodopa-responsive and fulfilled the UK Brain Bank Clinical Criteria for a diagnosis of clinical PD (Hughes, Ben-Shlomo et al. 1992) with no other neurodegenerative conditions. </p> <p>Cells were not extracted. Tissue sections were cut from FFPE blocks of post-mortem human midbrains at 6µm on a rotary microtome (HistoCore MULTICUT, Leica Biosystems) and mounted on Series 2 adhesive microscope slides (Trajan Scientific Medical, AU) for processing for spatial trranscriptomics. To remove the paraffin, slides were incubated in the oven at 60°C for 1hr and then submerged in HistoChoice Clearing Agent (Sigma-Aldrich, H2779) for 2x7mins, followed by rehydration in decreasing ethanol concentrations (100% ethanol for 2x3mins, 95% ethanol for 3mins, 70% ethanol for 3mins) and distilled H2O for 3mins. </p> <p>Tissue sections were immunohistochemically stained for tyrosine hydroxylase and Regions of Interest (ROIs) processed following Nanostring GeoMx® Digital Spatial Profiler using the manufacturer’s instructions. Libraries were sequenced on Illumina Novaseq 6000 platform using NovaSeq SP 100 cycle kit (XP workflow, 27-8-8-27).</p> <p>This research was funded in whole or in part by Aligning Science Across Parkinson’s (ASAP-020505) through the Michael J. Fox Foundation for Parkinson’s Research (MJFF). For the purpose of open access, the author has applied a CC BY 4.0 public copyright license to all Author Accepted Manuscripts arising from this submission.</p>
Conserved and cell type-specific transcriptional responses to IFN-γ in the ventral midbrain
<p>FISH image quantification and pSTAT1-Y701 analysis of fig.4 </p>
Data from: Midbrain adaptation may set the stage for the perception of musical beat
Open the record for dataset details and reuse information.
microRNA counts from midbrain (ENCSR257PBL)
GEO Series GSE220349. Mus musculus. 2 samples. Type: Non-coding RNA profiling by array.
microRNA-seq from midbrain (ENCSR863FYW)
GEO Series GSE82982. Mus musculus. 2 samples. Type: Non-coding RNA profiling by high throughput sequencing.
ChIP-seq from midbrain (ENCSR415FCU)
GEO Series GSE82674. Mus musculus. 2 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Single Cell RNA-seq Study of Midbrain and Dopaminergic Neuron Development in Mouse, Human, and Stem Cells
GEO Series GSE76381. Homo sapiens; Mus musculus. 6179 samples. Type: Expression profiling by high throughput sequencing.
total RNA-seq from midbrain (ENCSR557RMA)
GEO Series GSE78406. Mus musculus. 2 samples. Type: Expression profiling by high throughput sequencing.
ChIP-seq from midbrain (ENCSR322XHD)
GEO Series GSE82600. Mus musculus. 2 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Molecular diversity and migration of GABAergic neurons in the developing ventral midbrain
GEO Series GSE268378. Mus musculus. 9 samples. Type: Expression profiling by high throughput sequencing.
single cell RNA-seq from midbrain (ENCSR026ZRP)
GEO Series GSE78318. Mus musculus. 2 samples. Type: Expression profiling by high throughput sequencing.
Single-cell transcriptional and functional analysis of human dopamine neurons in 3D fetal ventral midbrain organoid like cultures
GEO Series GSE192405. Homo sapiens. 13 samples. Type: Expression profiling by high throughput sequencing.
ChIP-seq from midbrain (ENCSR525BTK)
GEO Series GSE82760. Mus musculus. 2 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
microRNA counts from midbrain (ENCSR378DMT)
GEO Series GSE220363. Mus musculus. 2 samples. Type: Non-coding RNA profiling by array.
A de novo Missense Mutation in PPP2R5D Alters Dopamine Pathways and Morphology of iPSC-derived Midbrain Neurons
GEO Series GSE238213. Homo sapiens. 24 samples. Type: Expression profiling by high throughput sequencing.
ChIP-seq from midbrain (ENCSR817FFF)
GEO Series GSE82956. Mus musculus. 2 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Translational profiling of hypothalamic and midbrain neurons that project to the nucleus accumbens.
GEO Series GSE55800. Mus musculus. 6 samples. Type: Expression profiling by high throughput sequencing.
miR-182 and miR-183 act as GDNF mimics in midbrain neurons
GEO Series GSE109066. Mus musculus. 20 samples. Type: Non-coding RNA profiling by high throughput sequencing.
microRNA-seq from midbrain (ENCSR680TRJ)
GEO Series GSE82875. Mus musculus. 2 samples. Type: Non-coding RNA profiling by high throughput sequencing.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.