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86 results for “optogenetic”
Data set for "Optogenetic stimulation of cortex to map evoked whisker movements in awake head-restrained mice"
<p>Data set for: Auffret M, Ravano VL, Rossi GMC, Hankov N, Petersen MFA, Petersen CCH (2017) Optogenetic stimulation of cortex to map evoked whisker movements in awake head-restrained mice. Neuroscience, http://dx.doi.org/10.1016/j.neuroscience.2017.04.004</p> <p>There are 9 files in this data upload:</p> <ol> <li>'2017_Auffret_Neuroscience.pdf' - this is a pdf version of the online publication.</li> <li>'Auffret_data.mat' - this is a Matlab data structure, which contains all the data for the publication.</li> <li>'Auffret_data.npy' - this is a Python data structure, which contains all the data for the publication. The Python data was generated from 'Auffret_data.mat' by 'DataViewer.py'.</li> <li>'Auffret_data.xlsx' - this is an Excel file, which contains all the data for the publication. This Excel file was generated from 'Auffret_data.mat'.</li> <li>'DataViewer.fig' - this is a Matlab Figure file, which is the GUI layout for 'DataViewer.m'.</li> <li>'DataViewer.m' - this is a Matlab Code, which displays the data contained in 'Auffret_data.mat'.</li> <li>'DataViewer.py' - this is a Python Code, which generates 'Auffret_data.npy' from 'Auffret_data.mat', and displays an example trial.</li> <li>'FigureViewer.fig' - this is a Matlab Figure file, which is the GUI layout for 'FigureViewer.m'.</li> <li>'FigureViewer.m' - this is a Matlab Code, which analyses the data in 'Auffret_data.mat', and displays the results in the same way as the published figures (Auffret et al., 2017).</li> </ol>
Functional networks of inhibitory neurons orchestrate synchrony in the hippocampus: optogenetical stimulation data
<p>This dataset contains 2-photon calcium imaging data from the paper 'Functional networks of inhibitory neurons orchestrate synchrony in the hippocampus'. This is the calcium imaging data from CA1 pyramidal cells and interneurons, including both spontaneous activity and activity in response to optogenetic stimulation.</p> <p><strong>Data organization</strong></p> <p>This dataset contains all the data related to the all-optical part of the paper and was analyzed using the code from the <a href="https://gitlab.com/cossartlab/bocchio-vorobyev-et-al-2023/-/tree/main/Optogenetical%20stimulation?ref_type=heads">lab repository</a>. The original calcium imaging movies are excluded due to size limitations.</p> <p><strong>Further information</strong></p> <p>Please email vorobev[a t]phystech.edu if you need further information on the data or if you wish to access the raw calcium imaging movies (not uploaded here due to storage limitations).</p>
raw data for Optogenetic Stimulation of Prelimbic Pyramidal Neurons Maintains Fear Memories and Modulates Amygdala Pyramidal Neuron Transcriptome
<p>Figure Legend </p> <p>Modulation of cellular excitability of Prelimbic (PrL) pyramidal neurons by optogenetic stimulation. (<strong>A</strong>) Representative traces in current-clamp configuration reporting evoked firing activity triggered by a series of depolarizing current steps (0 to 400 pA) applied to PrL pyramidal neurons of SHAM FEAR (black, <em>n</em> = 8 neurons from 5 mice), OPTO FEAR (red, <em>n</em>= 8 neurons from 5 mice), and No-EX (green, <em>n</em> = 5 neurons from 3 mice) groups. The cumulative plot shows the changes in firing activity. (<strong>B</strong>) Representative traces of PrL pyramidal neurons of SHAM FEAR (black, <em>n</em> = 8 neurons from 5 mice), OPTO FEAR (red, <em>n</em>= 8 neurons from 5 mice), and No-EX (green, <em>n</em> = 5 neurons from 3 mice) groups showing the firing activity triggered by linear depolarization from 0 to 800 pA. Graph (on the right) reports the effects of optogenetic stimulation on rheobase value. Namely, PrL pyramidal neurons of OPTO FEAR and No-EX groups recorded after optogenetic stimulation showed a clear reduction in the rheobase value in comparison to neurons of SHAM FEAR group (* at least <em>p</em>= 0.01). (<strong>C</strong>) Representative traces of Excitatory Post-Synaptic Currents (EPSC) of PrL pyramidal neurons of SHAM FEAR (black, <em>n</em> = 8 neurons from 5 mice), OPTO FEAR (red, <em>n</em>= 8 neurons from 5 mice), and No-EX (green, <em>n</em> = 5 neurons from 3 mice) groups. Graph plot (in the middle) and cumulative curve (on the right) depict the clear increase in firing frequency in PrL pyramidal neurons of OPTO FEAR and No-EX groups (* at least <em>p</em> = 0.01). (<strong>D</strong>) Graphs and cumulative curves report no significant differences in cellular excitability in PrL pyramidal neurons of SHAM NOT FEAR (black) and OPTO NOT FEAR (blue) groups. Data are reported as median with interquartile range.</p>
Spatio-temporal, optogenetic control of gene expression in organoids
<p>Organoids derived from stem cells become increasingly important to study human development and to model disease. However, methods are needed to control and study spatio-temporal patterns of gene expression in organoids. To this aim, we combined optogenetics and gene perturbation technologies to activate or knock-down RNA of target genes, at single-cell resolution and in programmable spatio-temporal patterns. To illustrate the usefulness of our approach, we locally activated Sonic Hedgehog (<em>SHH</em>) signaling in an organoid model for human neurodevelopment. High-resolution spatial transcriptomic and single-cell analyses showed that this local induction was sufficient to generate stereotypically patterned organoids in three dimensions and revealed new insights into <em>SHH</em>’s contribution to gene regulation in neurodevelopment.</p> <p>With this study, we propose optogenetic perturbations in combination with spatial transcriptomics as a powerful technology to reprogram and study cell fates and tissue patterning in organoids.</p>
Data from: Functional PET/MRI reveals active inhibition of neuronal activity during optogenetic activation of the nigrostriatal pathway
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Computational simulations show proof-of-concept for optogenetic suppression of ectopic activity in cardiac stem cell therapy
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Data from: An essential experimental control for functional connectivity mapping with optogenetics
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BIDS Data for "Effects of Acute and Chronic Reuptake Inhibitionon on Optogenetically Induced Serotonergic Activity"
<p>Base data package for the “Effects of Acute and Chronic Reuptake Inhibitionon Optogenetically Induced Serotonergic Activity” article, formatted corresponding to the Brain Imaging Data Structure.</p>
Data from: Spatiotemporally precise optogenetic activation of sensory neurons in freely walking Drosophila
<p>Previous work has characterized how walking <i>Drosophila</i> coordinate the movements of individual limbs (DeAngelis, Zavatone-Veth, and Clark, 2019). To understand the circuit basis of this coordination, one must characterize how sensory feedback from each limb affects walking behavior. However, it has remained difficult to manipulate neural activity in individual limbs of freely moving animals. Here, we demonstrate a simple method for optogenetic stimulation with body side-, body segment-, and limb-specificity that does not require real-time tracking. Instead, we activate at random, precise locations in time and space and use post hoc analysis to determine behavioral responses to specific activations. Using this method, we have characterized limb coordination and walking behavior in response to transient activation of mechanosensitive bristle neurons and sweet-sensing chemoreceptor neurons. Our findings reveal that activating these neurons has opposite effects on turning, and that activations in different limbs and body regions produce distinct behaviors.</p>
A voltage-dependent fluorescent indicator for optogenetic applications, archaerhodopsin-3: Structure and optical properties from in silico modeling
<p>seq.fasta and P96787_1UAZ.fasta are the input files for I-TASSER suite.</p> <p>The command of running I-TASSER suite:<br> path-to-I-TASSER-dir/I-TASSERmod/runI-TASSER.pl -pkgdir path-to-I-TASSER-dir -libdir path-to-I-TASSER-lib-dir -seqname P96787 -datadir path-to-workdir -outdir path-to-outdir -java_home /usr/ -restraint2 P96787_1UAZ.fasta</p> <p>For detailed data please refer to I-TASSER documentation.</p> <p>The P96787_1UAZ_IT.zip is an archieve with I-TASSER output for the best achaerhodopsin-3 prediciton.</p> <p>SCRIPTS_GENERAL.zip contains all the scripts for the structure postprocessing: addition of hydrogen atoms,<br> chromophore insertion and equilibration, internal waters addition.</p> <p>P96787_wi.pdb is a final prepared structure.</p> <p>Input files for spectra calculations are rhodopsin_gaussian.inp and rhodopsin_orca.inp.</p> <p> </p>
Supplementary information for: "A voltage-dependent fluorescent indicator for optogenetic applications, archaerhodopsin-3: Structure and optical properties from in silico modeling".
<p>This is supplementary data for F1000Research article: A voltage-dependent fluorescent indicator for optogenetic applications, archaerhodopsin-3: Structure and optical properties from in silico modeling.</p> <p>Here are files for modeling archaerhodopsin-3 with I-TASSER, Medeller and RosettaCM algorithms, structure postprocessing and spectra calculations.</p>
Data for: Optogenetic inhibition of behavior with anion channelrhodopsins
<p>Data for: Potent optogenetic inhibition of behavior with anion channelrhodopsins, a study available at bioRxiv https://doi.org/10.1101/082255</p> <p><strong>Abstract</strong><br> Optogenetics employs light exposure to manipulate physiology in genetically modified organisms. There are abundant tools for optogenetic excitation, but the limitations of current photo-inhibitors present an obstacle to demonstrating the necessity of neuronal circuits. Here we show that anion channelrhodopsins can be used to specifically and rapidly inhibit neural systems involved in Drosophila locomotion, wing expansion, memory retrieval and gustation, demonstrating their broad utility to the circuit analysis of behavior.</p>
Chemo- and optogenetic activation of hypothalamic Foxb1-expressing neurons and their terminal endings in the rostral-dorsolateral PAG leads to tachypnea, bradycardia, and immobility
<p>Foxb1-expressing neurons occur in the dorsal premammillary nucleus (PMd) and further rostrally in the parvafox nucleus, a longitudinal cluster of neurons in the lateral hypothalamus of rodents. The descending projection of these Foxb1+ neurons end in the dorsolateral part of the periaqueductal gray (dlPAG). The functional role of the Foxb1+ neuronal subpopulation in the PMd and the parvafox nucleus remains elusive. In this study, the activity of the Foxb1+ neurons and of their terminal endings in the dlPAG was selectively altered by employing chemo- and optogenetic tools. Our results show that in whole-body barometric plethysmography, hM3Dq-mediated, global Foxb1+ neuron excitation activates respiration. Time-resolved optogenetic gain-of-function manipulation of the terminal endings of Foxb1+ neurons in the rostral third of the dlPAG leads to abrupt immobility and bradycardia. Chemogenetic activation of Foxb1+ cell bodies and ChR2-mediated excitation of their axonal endings in the dlPAG led to a phenotypical presentation congruent with a "freezing-like" situation during innate defensive behavior. The authors have no relevant financial or non-financial interests to disclose. This work was supported by the Swiss National Foundation grant 31003A_160325 to Marco R. Celio.</p>
Mechanoluminescent nanomaterials for optogenetic neuromodulation-Part I
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Optogenetic activation of striatal D1R and D2R cells differentially engages downstream connected areas beyond the basal ganglia
<p>This dataset supports the Cell Reports publication entitled '<em>Optogenetic activation of striatal D1/D2 medium spiny neurons differentially engages downstream connected areas beyond the basal ganglia</em>' (https://doi.org/10.1016/j.celrep.2021.110161). Please refer to this publication for detailed information. </p> <p>The dataset contains functional (GE-BOLD) and anatomical (T1-weighted) scans of a total of 34 subjects (Cre-mouse lines Drd1-Cre, Drd2-Cre, A2A-Cre, and wildtype mice) in NIFTI format, multiplied by 10. The 'StimulationProtocol' text file specifies the precise onset (in seconds) and duration (in seconds) of the optogenetic stimulation during a 480 seconds functional scan. The 'SubjectDetails' file lists the subject IDs, their gender, their genotype, the number of functional scans, and whether they have an associated anatomical scan.</p>
Data for: Optogenetic olfactory behavior depends on illumination characteristics
<p><strong>Abstract</strong></p> <p>Optogenetics has become an important tool to study behavior: it enables neuroscientists to infer causations by examining animal behavior after activating genetically circumscribed neurons with light. Light-induced activity is profoundly affected by illumination parameters used in experiments, such as intensity, duration, and frequency. How sensitive behavioral outcomes to light-dependent spike changes has not been extensively studied. Here, we investigated the hypothesis that light frequency would alter optogenetically induced behaviours. To test this, we activated olfactory receptor neurons (ORNs) in Drosophila by using either static- or pulsed-light stimuli. Static- and pulsed-light stimulations elicited distinct valence responses (attraction, aversion, neutral) to artificial activity in ORNs. Our results demonstrate the importance of light frequency for interpreting behavioral experiments accurately, and suggest that multiple light parameters should be tested before generalizing behavioral experiment results.</p>
Data and code for: Cellular-resolution optogenetics reveals attenuation-by-suppression in visual cortical neurons
<p>Data and accompanying analysis code to generate main figures from "Cellular-resolution optogenetics reveals attenuation-by-suppression in visual cortical neurons" in PNAS.</p> <p> </p> <p> </p>
Single unit electrophysiology of optogenetically identified dopamine neurons in classical conditioning with probabilistic outcome of reward and punishment
<p>We collected single-unit data (.mat file) from optogenetically identified dopamine neurons in the lateral VTA in mice. These dopamine neurons were recorded while animals performed 4 different variation of classical conditioning tasks with different ratio of probabilistic outcomes of water reward and aversive air puff. In one task, one cue was associated with both water and puff in a probabilistic manner.</p>
Single unit electrophysiology of optogenetically identified dopamine neurons in classical conditioning with probabilistic outcome of reward and punishment
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Data for: Whole brain in situ mapping of neuronal activation in Drosophila during social behaviors and optogenetic stimulation
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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.