Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
34
datasets available to search
ShareScore release 0.7.1
Dataset results
34 results for “VTA”
BIDS Data for "A Whole-Brain Map and Assay Parameter Analysis of Mouse VTA Dopaminergic Activation"
<p>Base data package for the “"A Whole-Brain Map and Assay Parameter Analysis of Mouse VTA Dopaminergic Activation” article, formatted corresponding to the Brain Imaging Data Structure.</p>
A VTA to basal amygdala dopamine projection contributes to signal salient somatosensory events during fear learning
<p>This dataset represents the raw data that gave rise to the study by Tang et al., J. Neuroscience 2020 (DOI: 10.1523/JNEUROSCI.1796-19.2020). Please refer to the original publication regarding experimental design and methodological details of data acquisition and analysis. Below we supply information on the provided metadata files (which, in turn, refer to individual raw data files), and essential details on the specific data formats.</p> <ol> <li>raw data is organized in the datasets related to the Figs. 1H-L, 1M, 3B-C, 2, 4G-H, 5D-E, 5H-I of the paper (Tang et al., 2020);</li> <li>the metadata for each individual dataset, which lists individual data filenames from the respective dataset, are stored in separate “.csv” files, one per each dataset. Field separator: comma;</li> <li>individual metadata files for each dataset are described in the master metadata file “metadata_master.csv”. Field separator: comma;</li> <li>widefield fluorescent images of single coronal slices containing VTA (Fig. 1H-M) were converted from the proprietary format of Olympus slide scanning microscope into composite TIFF format readable by FIJI/ImageJ (<a href="https://fiji.sc/">https://fiji.sc/</a> or <a href="https://imagej.net/Fiji/Downloads">https://imagej.net/Fiji/Downloads</a>). Image stacks covering the injection area of CTB into BA are provided in single multi-plane TIFF files, one per animal. Unless specified in the metadata file, the information on pixel resolution is embedded inside the individual image files as TIFF metadata. Attribution of fluorescent probes to the color channels is given in the corresponding metadata files; AP positions refer to Franklin KB, Paxinos G (2016) The mouse brain in stereotaxic coordinates, Ed 4. San Diego: Elsevier/Academic;</li> <li>confocal fluorescent image stacks acquired from single coronal slices containing VTA (Fig. 3B-C) are provided in the original format “.lsm” written by a confocal software Zen (Carl Zeiss). Besides the original Zen software, this format can be readily imported into FIJI/ImageJ using built-in converters “LSM…” or “Bio-Formats”. All the metadata containing imaging parameters is embedded in this format and can be accessed from FIJI/ImageJ after importing the stack. Attribution of fluorescent probes to the color channels is given in the corresponding “.csv” metadata file; AP positions refer to Franklin and Paxinos (2016);</li> <li>video recordings of animal behavior are provided as “.wmv” files, unmodified from the original version created by the acquisition software VideoFreeze (MedAssociates Inc). Video stream parameters: wmv3 codec, color space yuv420p, 320x240 pixels, bitrate 300 kb/s, 30 fps;</li> <li>timing patterns of the sound (CS) and of the footshock (US) applications during each day of fear conditioning protocol are provided in the respective “.csv” files: “day1_CS_timing.csv”, “day2_CS_timing.csv”, “day2_US_timing.csv”, “day3_CS_timing.csv”. The timestamps in these files are expressed in seconds relative to the start of the VideoFreeze video recordings (see p. 4 above). These patterns are in common for all the video recordings done on respective training days in every data subset (Figs. 2, 4-5);</li> <li>extracellular optrode recording data (Fig. 2) were converted from the original proprietary “.mcd” format of the MC_Rack software (Multichannel Systems) into the open HDF5 format “.h5” using the Multi Channel DataManager software (Multichannel Systems). We provide both the continuous recording data acquired during behavior sessions on days 1-3 of the fear learning protocol, as well as recordings of light-evoked spiking acquired during the opto-tagging sessions on each experimental day. In the latter, each of 8-10 consequently recorded data files contains individual triggered sweeps (from -50 to +50 ms), each centered around a single laser pulse (t=0 ms);</li> <li>the raw unfiltered electrode data is stored as a 32-bit integer matrix 16xN (16 - number of electrodes, N - number of sampling points @ 40 kHz) in the container Data->Recording_0->AnalogStream->Stream_1->ChannelData of the HDF5 files. Conversion factor to the units of volts for the raw values is 1.25e-6. Correspondence of the rows of the data matrix to the electrodes “E1”-“E16” is indexed by the string array Data->Recording_0->AnalogStream->Stream_1->I_Label. The electrodes were physically arranged into four tetrodes in following groups: E1-E4, E5-E8, E9-E12, E13-E16;</li> <li>timestamps for the continuous recordings, or for each of the triggered sweeps in case of opto-tagging, are stored in the 2D floating point array Data->Recording_0->AnalogStream->Stream_1->ChannelDataTimeStamps; the timestamp values are in microseconds;</li> <li>the timing of CS and US stimuli produced by the VideoFreeze software (see p. 5 above) was sampled as input digital triggers by the amplifier for extracellular recordings for precise synchronization between the optrode- and video recordings. These signals are stored as single bit changes in the 32-bits integer N-samples array Data->Recording_0->AnalogStream->Stream_0->ChannelData of the corresponding HDF5 files.</li> </ol>
Images of mouse VTA and SNc sections labeled for neurotransmitter phenotype markers via RNAscope
<p>48 coronal sections from 3 male and 3 female C57Bl/6J mice were labeled for mRNAs encoding the canonical vesicular transporters for dopamine (VMAT2), GABA (VGAT), and glutamate (VGLUT2). These sections were then imaged via confocal microscopy and saved as CZI files, editable with Zeiss Zen software. These image files include 'event marker' graphics, indicating where neurons positive for one or more of the above transporters are. </p> <p>The protocols used for sample preparation, labeling, imaging, and counting are linked in the Related Works section. </p> <p>Cell count data are organized by subregion (SUBREGION counts for R.csv), anterior-posterior (e.g. VGATVTA.csv), or anterior-posterior and medial-lateral distribution (e.g. 'snc triple.csv' or 'snc vmat2 AP and ML.csv').</p> <p>The R code provided uses these csv files to visualize expression patterns across VTA and SNc. </p>
Data from: Learning of probabilistic punishment as a model of anxiety produces changes in action but not punisher encoding in the dmPFC and VTA
<p>Previously, we developed a novel model for anxiety during motivated behavior by training rats to perform a task where actions executed to obtain a reward were probabilistically punished and observed that after learning, neuronal activity in the ventral tegmental area (VTA) and dorsomedial prefrontal cortex (dmPFC) represent the relationship between action and punishment risk (Park & Moghaddam, 2017). Here we used male and female rats to expand on the previous work by focusing on neural changes in the dmPFC and VTA that were associated with the learning of probabilistic punishment, and anxiolytic treatment with diazepam after learning. We find that adaptive neural responses of dmPFC and VTA during the learning of anxiogenic contingencies are independent from the punisher experience and occur primarily during the peri-action and reward period. Our results also identify peri-action ramping of VTA neural calcium activity, and VTA-dmPFC correlated activity, as potential markers for the anxiolytic properties of diazepam.</p>
Overlapping representations of food and social stimuli in VTA dopamine neurons
<p>2-photon imaging and behavioral data accompanying publication of "Overlapping representations of food and social stimuli in VTA dopamine neurons" (Lindsay Willmore, Adelaide Minerva, Ben Engelhard, Brenna McMannon, Nirja Oak, Stephan Thiberge, Malavika Murugan, Catherine Jensen Pena, Ilana Witten). This dataset contains all information required to recreate figures from the paper. </p>
Overlapping representations of food and social stimuli in VTA dopamine neurons
Open the record for dataset details and reuse information.
Data from: Learning of probabilistic punishment as a model of anxiety produces changes in action but not punisher encoding in the dmPFC and VTA
Open the record for dataset details and reuse information.
Dataset for "Dissociable Roles of the mPFC-to-VTA pathway in the control od Impulsive action and Risk-Related Decision-Making in Roman High- and Low-Avoidance Rats"
<p>This dataset corresponds to the study "Dissociable Roles of the mPFC-to-VTA Pathway in the Control of Impulsive Action and Risk-Related Decision-Making in Roman High- and Low-Avoidance Rats". In this study, we used Positron Emission Tomography with [18F]-Fluorodeoxyglucose to evaluate brain metabolic activity in Roman High- (RHA) and Low-avoidance (RLA) rats, which exhibit innate differences in impulsivity. Notably, we used a viral-based intersectional chemogenetic strategy to isolate the role of the mPFC-to-VTA pathway in controlling impulsive behaviors. We selectively activated the mPFC-to-VTA pathway in RHA rats and inhibited it in RLA rats, assessing the effects on impulsive action and RDM in the rat gambling task. Our results showed that RHA rats displayed higher impulsive action, less optimal decision-making, and lower cortical activity than RLA rats at baseline. Chemogenetic activation of the mPFC-to-VTA pathway reduced impulsive action in RHA rats, whereas chemogenetic inhibition had the opposite effect in RLA rats. However, these manipulations did not affect RDM. Our findings suggest a dissociable role of the mPFC-to-VTA pathway in impulsive action and RDM, highlighting its potential as a target for investigating impulsivity-related disorders.</p> <p><strong>Contributions for usage of this data in publications:</strong></p> <p>If you publish any work using these data, please cite this repository and the associated publication.</p>
The ion channel mechanisms of the subthreshold inward depolarizing currents in the mice VTA dopaminergic neurons and their roles in the depression-like behavior
Open the record for dataset details and reuse information.
An endogenous GLP-1 circuit engages VTA GABA neurons to regulate mesolimbic dopamine neurons and attenuate cocaine seeking
Open the record for dataset details and reuse information.
Opposite effects of stress on effortful motivation in high and low anxiety are mediated by CRHR1 in the VTA
<p>Rat DNA sequencing data</p>
The PIVATAL Study -Study of Ventricular Arrhythmia (VTA) Ablation in Left Ventricular Assist Device (LVAD) Patients
ClinicalTrials.gov study NCT05034432. IPD Sharing: NO. Countries: 1. Publications: 0.
Stress resilience is associated with transcriptional remodeling in the VTA
GEO Series GSE303538. Mus musculus. 34 samples. Type: Expression profiling by high throughput sequencing.
Molecular profiling of prelimbic projections to NAc, BLA, and VTA using vTRAP
GEO Series GSE104943. Mus musculus. 16 samples. Type: Expression profiling by high throughput sequencing.
Profiling of mRNA transcriptomic changes using RNA-seq in postmortem ventral tegmental area (VTA) of subjects with alcohol use disorder
GEO Series GSE182649. Homo sapiens. 24 samples. Type: Expression profiling by high throughput sequencing.
Overlapping representations of food and social stimuli in VTA dopamine neurons
GEO Series GSE235149. Mus musculus. 10 samples. Type: Expression profiling by high throughput sequencing.
RNAseq of human SNc and VTA midbrain dopamine neurons isolated from post mortem material of control subjects and Parkinson's Disease patients using laser capture microdisection.
GEO Series GSE114918. Homo sapiens. 52 samples. Type: Expression profiling by high throughput sequencing.
Gene expression in the human VTA of cases with alcohol abuse
GEO Series GSE9058. Homo sapiens. 12 samples. Type: Expression profiling by array.
RNA-sequencing in rat ventral tegmental area (VTA) following chronic ethanol and withdrawal
GEO Series GSE233921. Rattus norvegicus. 18 samples. Type: Expression profiling by high throughput sequencing.
Ventral Tegmental Area (VTA) Self-Activation in Attention Deficit Hyperactivity Disorder (ADHD)
ClinicalTrials.gov study NCT02723708. IPD Sharing: NO. Countries: 1. Publications: 0.
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.