cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25378/janelia.13469970
title: Isotropic 3D electron microscopy data of HeLa cell treated with H89 for correlative light and electron microscopy studies (jrc_hela-h89-2)

description: Cellular versatility depends on the accurate trafficking of diverse proteins to their organellar destinations. For the secretory pathway (followed by ~30% of all proteins), the physical nature of the vessel conducting the first portage (ER→Golgi) is unclear. We provide a dynamic 3D view of early secretory compartments in mammalian cells with unprecedented isotropic resolution and precise protein localization using whole-cell, focused ion beam scanning electron microscopy with cryo-structured illumination microscopy and live-cell synchronized cargo release approaches. Rather than vesicles alone, the ER spawns an elaborate, interwoven tubular network of contiguous lipid bilayers (the ER exit site) for protein export. This receptacle is capable of extending microns along microtubules while still connected to ER by a thin neck. COPII localizes to the neck region and dynamically regulates cargo entry from ER, while COPI acts more distally, escorting the detached, accelerating tubular entity on its way to joining the Golgi apparatus through microtubule-directed movement.<br><br>Sample: Interphase HeLa cell overexpressing mEmerald-Sec23 frozen 9 min post 50 µM H89 addition.Protocol: High pressure freezing, freeze-substitution resin embedding with 1% OsO4 0.1% UA 3% H2O in acetone; resin embedding in Eponate 12.Contributions: Sample provided by Aubrey Weigel and Chi-Lun Chang (HHMI/Janelia), prepared for imaging by Gleb Shtengel (HHMI/Janelia), with imaging and post-processing by C. Shan Xu (HHMI/Janelia).Dataset ID: jrc_hela-h89-2Final voxel size (nm): 8.0 x 8.0 x 8.0 (X, Y, Z)Dimensions (µm): 50 x 8 x 98.86 (X, Y, Z)Acquisition date: 2020-10-15Visualization Website: https://openorganelle.janelia.org/datasets/jrc_hela-h89-2Publication Reference: Weigel et al., (2020)
DOI: 10.25378/janelia.13469970.v1
title: Isotropic 3D electron microscopy data of HeLa cell treated with H89 for correlative light and electron microscopy studies (jrc_hela-h89-2)

description: Cellular versatility depends on the accurate trafficking of diverse proteins to their organellar destinations. For the secretory pathway (followed by ~30% of all proteins), the physical nature of the vessel conducting the first portage (ER→Golgi) is unclear. We provide a dynamic 3D view of early secretory compartments in mammalian cells with unprecedented isotropic resolution and precise protein localization using whole-cell, focused ion beam scanning electron microscopy with cryo-structured illumination microscopy and live-cell synchronized cargo release approaches. Rather than vesicles alone, the ER spawns an elaborate, interwoven tubular network of contiguous lipid bilayers (the ER exit site) for protein export. This receptacle is capable of extending microns along microtubules while still connected to ER by a thin neck. COPII localizes to the neck region and dynamically regulates cargo entry from ER, while COPI acts more distally, escorting the detached, accelerating tubular entity on its way to joining the Golgi apparatus through microtubule-directed movement.<br><br>Sample: Interphase HeLa cell overexpressing mEmerald-Sec23 frozen 9 min post 50 µM H89 addition.Protocol: High pressure freezing, freeze-substitution resin embedding with 1% OsO4 0.1% UA 3% H2O in acetone; resin embedding in Eponate 12.Contributions: Sample provided by Aubrey Weigel and Chi-Lun Chang (HHMI/Janelia), prepared for imaging by Gleb Shtengel (HHMI/Janelia), with imaging and post-processing by C. Shan Xu (HHMI/Janelia).Dataset ID: jrc_hela-h89-2Final voxel size (nm): 8.0 x 8.0 x 8.0 (X, Y, Z)Dimensions (µm): 50 x 8 x 98.86 (X, Y, Z)Acquisition date: 2020-10-15Visualization Website: https://openorganelle.janelia.org/datasets/jrc_hela-h89-2Publication Reference: Weigel et al., (2020)
DOI: 10.25378/janelia.13546157
title: Dataset supporting "Targeted photostimulation uncovers circuit motifs supporting short-term memory"

description: Dataset supporting paper: "Targeted photostimulation uncovers circuit motifs supporting short-term memory"<br>We used two-photon photostimulation and imaging to measure coupling between functionally characterized motor cortex neurons in mice performing a memory guided response task. <br>Data structure and parameters are described in included data structure file.<br><br>Paper Abstract: Short-term memory is associated with persistent neural activity that is maintained by positive feedback between neurons. To explore the neural circuit motifs that produce memory-related persistent activity, we measured coupling between functionally characterized motor cortex neurons, in mice performing a memory guided response task. Targeted 2-photon photostimulation of small (&lt; 10) groups of neurons produced sparse calcium responses in coupled neurons over approximately 100 micrometers. Neurons with similar task-related selectivity were preferentially coupled. Photostimulating different groups of neurons modulated activity in different subpopulations of coupled neurons. Responses of stimulated and coupled neurons persisted for seconds, far outlasting the duration of the photostimuli. Photostimuli produced behavioral biases that were predictable based on the selectivity of the perturbed neuronal population, even though photostimulation preceded the behavioral response by seconds. Our results suggest that memory-related neural circuits contain intercalated recurrently connected modules, which can independently maintain selective persistent activity.
DOI: 10.25378/janelia.13546157.v1
title: Dataset supporting "Targeted photostimulation uncovers circuit motifs supporting short-term memory"

description: Dataset supporting paper: "Targeted photostimulation uncovers circuit motifs supporting short-term memory"<br>We used two-photon photostimulation and imaging to measure coupling between functionally characterized motor cortex neurons in mice performing a memory guided response task. <br>Data structure and parameters are described in included data structure file.<br><br>Paper Abstract: Short-term memory is associated with persistent neural activity that is maintained by positive feedback between neurons. To explore the neural circuit motifs that produce memory-related persistent activity, we measured coupling between functionally characterized motor cortex neurons, in mice performing a memory guided response task. Targeted 2-photon photostimulation of small (&lt; 10) groups of neurons produced sparse calcium responses in coupled neurons over approximately 100 micrometers. Neurons with similar task-related selectivity were preferentially coupled. Photostimulating different groups of neurons modulated activity in different subpopulations of coupled neurons. Responses of stimulated and coupled neurons persisted for seconds, far outlasting the duration of the photostimuli. Photostimuli produced behavioral biases that were predictable based on the selectivity of the perturbed neuronal population, even though photostimulation preceded the behavioral response by seconds. Our results suggest that memory-related neural circuits contain intercalated recurrently connected modules, which can independently maintain selective persistent activity.
DOI: 10.25378/janelia.14143118
title: anm454597 Cell 0 of "Simultaneous Voltron (1.0) imaging and whole-cell patch-clamp recordings of somatosensory cortex layer 1 interneurons in vivo."

description: This cell is a part of the collection: https://doi.org/10.25378/janelia.c.5325254 Please see collection for description, related datasets, and citation for dataset collection.
DOI: 10.25378/janelia.14143118.v1
title: anm454597 Cell 0 of "Simultaneous Voltron (1.0) imaging and whole-cell patch-clamp recordings of somatosensory cortex layer 1 interneurons in vivo."

description: This cell is a part of the collection: https://doi.org/10.25378/janelia.c.5325254 Please see collection for description, related datasets, and citation for dataset collection.
DOI: 10.25378/janelia.14143643
title: anm456462 Cell 8 of "Simultaneous Voltron (1.0) imaging and whole-cell patch-clamp recordings of somatosensory cortex layer 1 interneurons in vivo."

description: This cell is a part of the collection: https://doi.org/10.25378/janelia.c.5325254 Please see collection for description, related datasets, and citation for dataset collection.
DOI: 10.25378/janelia.14143862
title: anm456462 Cell 5 of "Simultaneous Voltron (1.0) imaging and whole-cell patch-clamp recordings of somatosensory cortex layer 1 interneurons in vivo."

description: This cell is a part of the collection: https://doi.org/10.25378/janelia.c.5325254 Please see collection for description, related datasets, and citation for dataset collection.
DOI: 10.25378/janelia.14143862.v1
title: anm456462 Cell 5 of "Simultaneous Voltron (1.0) imaging and whole-cell patch-clamp recordings of somatosensory cortex layer 1 interneurons in vivo."

description: This cell is a part of the collection: https://doi.org/10.25378/janelia.c.5325254 Please see collection for description, related datasets, and citation for dataset collection.
DOI: 10.25378/janelia.14143997
title: anm456462 Cell 6 of "Simultaneous Voltron (1.0) imaging and whole-cell patch-clamp recordings of somatosensory cortex layer 1 interneurons in vivo."

description: This cell is a part of the collection: https://doi.org/10.25378/janelia.c.5325254 Please see collection for description, related datasets, and citation for dataset collection.
DOI: 10.25378/janelia.14150360
title: anm456462 Cell 3 of "Simultaneous Voltron (1.0) imaging and whole-cell patch-clamp recordings of somatosensory cortex layer 1 interneurons in vivo."

description: This cell is a part of the collection: https://doi.org/10.25378/janelia.c.5325254 Please see collection for description, related datasets, and citation for dataset collection.
DOI: 10.25378/janelia.14150360.v1
title: anm456462 Cell 3 of "Simultaneous Voltron (1.0) imaging and whole-cell patch-clamp recordings of somatosensory cortex layer 1 interneurons in vivo."

description: This cell is a part of the collection: https://doi.org/10.25378/janelia.c.5325254 Please see collection for description, related datasets, and citation for dataset collection.
DOI: 10.25378/janelia.14151044
title: anm456462 Cell 4 of "Simultaneous Voltron (1.0) imaging and whole-cell patch-clamp recordings of somatosensory cortex layer 1 interneurons in vivo."

description: This cell is a part of the collection: https://doi.org/10.25378/janelia.c.5325254 Please see collection for description, related datasets, and citation for dataset collection.
DOI: 10.25378/janelia.14151044.v1
title: anm456462 Cell 4 of "Simultaneous Voltron (1.0) imaging and whole-cell patch-clamp recordings of somatosensory cortex layer 1 interneurons in vivo."

description: This cell is a part of the collection: https://doi.org/10.25378/janelia.c.5325254 Please see collection for description, related datasets, and citation for dataset collection.
DOI: 10.25378/janelia.14156372
title: anm462149 Cell 3 of "Simultaneous Voltron (1.0) imaging and whole-cell patch-clamp recordings of somatosensory cortex layer 1 interneurons in vivo."

description: This cell is a part of the collection: https://doi.org/10.25378/janelia.c.5325254 Please see collection for description, related datasets, and citation for dataset collection.
DOI: 10.25378/janelia.14156372.v1
title: anm462149 Cell 3 of "Simultaneous Voltron (1.0) imaging and whole-cell patch-clamp recordings of somatosensory cortex layer 1 interneurons in vivo."

description: This cell is a part of the collection: https://doi.org/10.25378/janelia.c.5325254 Please see collection for description, related datasets, and citation for dataset collection.
DOI: 10.25378/janelia.14156609
title: anm462149 Cell 1 of "Simultaneous Voltron (1.0) imaging and whole-cell patch-clamp recordings of somatosensory cortex layer 1 interneurons in vivo."

description: This cell is a part of the collection: https://doi.org/10.25378/janelia.c.5325254 Please see collection for description, related datasets, and citation for dataset collection.
DOI: 10.25378/janelia.14156609.v1
title: anm462149 Cell 1 of "Simultaneous Voltron (1.0) imaging and whole-cell patch-clamp recordings of somatosensory cortex layer 1 interneurons in vivo."

description: This cell is a part of the collection: https://doi.org/10.25378/janelia.c.5325254 Please see collection for description, related datasets, and citation for dataset collection.
DOI: 10.25378/janelia.14156735
title: anm463291 Cell 1 of "Simultaneous Voltron (1.0) imaging and whole-cell patch-clamp recordings of somatosensory cortex layer 1 interneurons in vivo."

description: This cell is a part of the collection: https://doi.org/10.25378/janelia.c.5325254 Please see collection for description, related datasets, and citation for dataset collection.
DOI: 10.25378/janelia.14156735.v1
title: anm463291 Cell 1 of "Simultaneous Voltron (1.0) imaging and whole-cell patch-clamp recordings of somatosensory cortex layer 1 interneurons in vivo."

description: This cell is a part of the collection: https://doi.org/10.25378/janelia.c.5325254 Please see collection for description, related datasets, and citation for dataset collection.
DOI: 10.25378/janelia.14157902
title: anm466769 Cell 2 of "Simultaneous Voltron (1.0) imaging and whole-cell patch-clamp recordings of somatosensory cortex layer 1 interneurons in vivo."

description: This cell is a part of the collection: https://doi.org/10.25378/janelia.c.5325254 Please see collection for description, related datasets, and citation for dataset collection.
DOI: 10.25378/janelia.14160881
title: anm466774 Cell 0 of "Simultaneous Voltron (1.0) imaging and whole-cell patch-clamp recordings of somatosensory cortex layer 1 interneurons in vivo."

description: This cell is a part of the collection: https://doi.org/10.25378/janelia.c.5325254 Please see collection for description, related datasets, and citation for dataset collection.<br>
DOI: 10.25378/janelia.14160881.v1
title: anm466774 Cell 0 of "Simultaneous Voltron (1.0) imaging and whole-cell patch-clamp recordings of somatosensory cortex layer 1 interneurons in vivo."

description: This cell is a part of the collection: https://doi.org/10.25378/janelia.c.5325254 Please see collection for description, related datasets, and citation for dataset collection.<br>
DOI: 10.25378/janelia.14161838
title: anm466774 Cell 2 of "Simultaneous Voltron (1.0) imaging and whole-cell patch-clamp recordings of somatosensory cortex layer 1 interneurons in vivo."

description: This cell is a part of the collection: https://doi.org/10.25378/janelia.c.5325254 Please see collection for description, related datasets, and citation for dataset collection.
DOI: 10.25378/janelia.14161838.v1
title: anm466774 Cell 2 of "Simultaneous Voltron (1.0) imaging and whole-cell patch-clamp recordings of somatosensory cortex layer 1 interneurons in vivo."

description: This cell is a part of the collection: https://doi.org/10.25378/janelia.c.5325254 Please see collection for description, related datasets, and citation for dataset collection.
DOI: 10.25378/janelia.15056133
title: Dataset of position tracking in 2AFC experiments supporting publication: "Dissociable contributions of phasic dopamine activity to reward and prediction"

description: A dataset collected to study mouse decision making and in particular whether exogenous stimulation of midbrain dopamine neurons can act as a discriminative cue or can directly bias decisions - relating to the paper "Dissociable contributions of phasic dopamine activity to reward and prediction".<br>Briefly, mice we placed in an enclosure with two reward ports located on a wall. The box was controlled by our hardware and software called Behavioral Control System (https://www.janelia.org/open-science/behavioral-control-system-box). We then used real-time tracking of mouse position (simple blob detection) to store trajectories of the mouse during the behavioral task. Associated code focuses on extracting these trajectories and analyzing choice behavior according to which port a mouse approached across a family of experiments with different combinations of cues (ontogenetic stimulation, room light, auditory tone).<br>
DOI: 10.25378/janelia.16663723
title: Non-preferred contrast responses Figure 4 illusory motion

description: This directory includes files to generate the data panels from Figure 4 from "Non-preferred contrast responses in the Drosophila motion pathways reveal a receptive field structure that explains a common visual illusion "<br>To generate the figure run Figure4Code from the source directory<br>## Files and variables<br>The files were generated with matlab r2020b<br>### allT4MinMotFirstComp.mat<br>This file contains 3 matlab variables<br>#### allMMTable<br>A matlab table referencing all the minimal motion stimuli that each T4 cell was presented with and the corresponding single flash stimuli that compose it used to index into the results structure<br>#### allSBTable<br>A matlab table referencing all the single bar flash stimuli that each T4 cell was presented width (used originally to simulate linear summation of the response)<br>#### minMotSt<br>matlab structure containing results from all the cells that were shown minimal motion stimuli. each field contains recordings from one cell, while the stimuli for each cell are organized by the index in allMMTable. (e.g. minMotSt(1).result(10) corresponds to the first cell in the table stimulus index 10)<br>### allT4MinMotFirstComp.mat<br>Same as above only for T5 cells<br>### Figure4Code<br>Matlab script for generating data panels in figure 4<br> See related materials supporting this publication in the collection at: https://doi.org/10.25378/janelia.c.5629663. <br>
DOI: 10.25378/janelia.8869115.v1
title: Recruitment of GABAergic Interneurons in the Barrel Cortex during Active Tactile Behavior

description: Cell type-specific recordings from fast-spiking (PV expressing), Sst, VIP neurons in the barrel cortex during active tactile behavior<br>Neural computation involves diverse types of GABAergic inhibitory interneurons that are integrated with excitatory (E) neurons into precisely structured circuits. To understand how each neuron type shapes sensory representations, we measured firing patterns of defined types of neurons in the barrel cortex while mice performed an active, whisker-dependent object localization task. Touch excited fast-spiking (FS) interneurons at short latency, followed by activation of E neurons and somatostatin-expressing (SST) interneurons. Touch only weakly modulated vasoactive intestinal polypeptide-expressing (VIP) interneurons. Voluntary whisker movement activated FS neurons in the ventral posteromedial nucleus (VPM) target layers, a subset of SST neurons and a majority of VIP neurons. Together, FS neurons track thalamic input, mediating feedforward inhibition. SST neurons monitor local excitation, providing feedback inhibition. VIP neurons are activated by non-sensory inputs, disinhibiting E and FS neurons. Our data reveal rules of recruitment for interneuron types during behavior, providing foundations for understanding computation in cortical microcircuits.<br>
DOI: 10.25378/janelia.16663705
title: Non-preferred contrast responses Figure 2 composite receptive field

description: Files to generate Figure 2 from "Non-preferred contrast responses in the Drosophila motion pathways reveal a receptive field structure that explains a common visual illusion"<br>To generate the figure run Figure2Code from the directory after adding the "supportingFunctions" folder to your path.<br>## Files and variables<br>The files were generated with matlab r2020b<br>### singleBarStT4.mat<br>This file contains a structure with all T4 cells responses to single bar flashes<br>Each field in the main structure contains the results from one cell organized supportingFunctions5 fields:.result - contains raw and processed recordings in a 4-D array(position, duration, width, value)<br>.positions - the positions that were assayed for the cell (before alignment).durations - flash durations that were assayed (in secs).width - bar widths that were assayed (in LED pixels).vals - bar contrast that was assayed<br>These can be used as a reference to the .result field.Note! the first and second dimensions for the result array are larger by one to include summary statistics<br>### singleBarStT5<br>Same as above only for T5 cells<br>### Figure2Code<br>Matlab script for generating figure 2, with all the necessary calculations<br> See related materials supporting this publication in the collection at: https://doi.org/10.25378/janelia.c.5629663.
DOI: 10.25378/janelia.16663705.v1
title: Non-preferred contrast responses Figure 2 composite receptive field

description: Files to generate Figure 2 from "Non-preferred contrast responses in the Drosophila motion pathways reveal a receptive field structure that explains a common visual illusion"<br>To generate the figure run Figure2Code from the directory after adding the "supportingFunctions" folder to your path.<br>## Files and variables<br>The files were generated with matlab r2020b<br>### singleBarStT4.mat<br>This file contains a structure with all T4 cells responses to single bar flashes<br>Each field in the main structure contains the results from one cell organized supportingFunctions5 fields:.result - contains raw and processed recordings in a 4-D array(position, duration, width, value)<br>.positions - the positions that were assayed for the cell (before alignment).durations - flash durations that were assayed (in secs).width - bar widths that were assayed (in LED pixels).vals - bar contrast that was assayed<br>These can be used as a reference to the .result field.Note! the first and second dimensions for the result array are larger by one to include summary statistics<br>### singleBarStT5<br>Same as above only for T5 cells<br>### Figure2Code<br>Matlab script for generating figure 2, with all the necessary calculations<br> See related materials supporting this publication in the collection at: https://doi.org/10.25378/janelia.c.5629663.
DOI: 10.25378/janelia.17777888.v1
title: Whole transcriptome annotation files

description: These are the manually corrected BRAKER annotations in GFF3 format, from Table S5 of "Gene structure-based homology search identifies highly divergent putative effector gene family", Stern and Han, BioRxiv https://doi.org/10.1101/2021.09.24.461719.<br>Please contact Clair Han at hanc@janelia.hhmi.org with any questions.<br><br> See related materials in collection at https://doi.org/10.25378/janelia.c.5778905.
DOI: 10.25378/janelia.17777888.v2
title: Whole transcriptome annotation files

description: These are the manually corrected BRAKER annotations in GFF3 format, from Table S5 of "Gene structure-based homology search identifies highly divergent putative effector gene family", Stern and Han, BioRxiv https://doi.org/10.1101/2021.09.24.461719.<br>Please contact Clair Han at hanc@janelia.hhmi.org with any questions.<br><br> See related materials in collection at https://doi.org/10.25378/janelia.c.5778905.
DOI: 10.25378/janelia.17783336
title: Classifier-identified bicycle genes lists

description: List of bicycle genes identified by the gene structure-based linear logistic regression classifier in each of 16 species, associated with Figure 1 from "Gene structure-based homology search identifies highly divergent putative effector gene family", Stern and Han, BioRxiv https://doi.org/10.1101/2021.09.24.461719.<br>Please contact Clair Han at hanc@janelia.hhmi.org with any questions.<br><br> See related materials in collection at https://doi.org/10.25378/janelia.c.5778905.