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Xenon's sedative effect is at least partly mediated by interaction with the cyclic nucleotide-binding domain (CNBD) of HCN2 channels expressed by thalamocortical neurons of the ventrobasal nucleus in mice
<p>Xenon (70%xenon, 30%O2) application in the last 10 min of the open field test manage to sedate wild-type mice but not HCN2EA. Wild-type mice in the xenon_wild-type video can be seen moving freely in the early minutes but the general activity starts to decrease sharply in the last 2 minutes and is absent between min 9 and 10 while HCN2EA mice in the xenon_HCN2EA can be seen moving throughout the entire time of the xenon gas mixture application.</p>
Human STING is a proton channel (Live-cell MGAT Super-Resolution Experiment)
<p>hTERT-immortalized BJ1 cells (ATCC CRL-2522) expressing SEP-mRuby3 targeted to cis/medial Golgi (MGAT) were transduced with pXPR023 (lentiCRISPRv2) expressing an sgRNA targeting STING and selected with 0.1 µg/mL puromycin for 5 days. Cells were then transduced with blasticidin-STING-miRFP680 and selected using 10 µg/mL blasticidin HCl for 5 days. Cells were plated in 96-well glass-bottom plates (Greiner Bio-One) at 6,000 cells/well. After 48 hours, cells were incubated in Fluorobrite DMEM (Thermo Fisher Scientific, cat. #A1896701) medium supplemented with 10% FBS, 1% Pen-strep, and 1x GlutaMAX (Thermo Fisher Scientific, cat. #35050061) and stimulated with 1 µM diABZI (Invivogen, #tlrl-diabzi). All images were acquired using an LSM980 with Airyscan2 (Zeiss) with 37°C with 5% CO2 incubation. 8 z-stacks were acquired with 0.15 µm z-step. Images were acquired using a 63X 1.40 NA DIC M27 objective with Immersol 518F 37°C oil. Acquired images were Airyscan processed and then analyzed as described in the image analysis section.</p> <p>Each frame represens one timepoint imaged every 5 minutes post diABZI treatment. Channels are: SEP (super-ecliptic pHluorin), mRuby3, and STING-miRFP680.</p> <p> </p>
Human STING is a proton channel (Live-cell GALT pH Measurement upon STING agonist treatment with or without C53)
<p>hTERT-immortalized BJ1 cells (ATCC CRL-2522) were transduced with lentiviral ratiometric reporters targeted to GALT constructed based on designs reported in Linders et al. <em>ACS Chem. Biol. </em>2022, with superecliptic pHluorin and mRuby3. Transduced cells were sorted based on mRuby3 expression using a Sony MA900 sorter. BJ1 SEP-mRuby3 cells were plated in 24-well glass-bottom plates (Greiner Bio-One) at 40,000 cells/well. After 48 hours, cells were stained for 45 minutes at 37°C with 0.5 µg/ml Hoechst 34580 (Thermo Fisher Scientific, cat. #H21486). Cells were then washed and incubated in Fluorobrite DMEM (Thermo Fisher Scientific, cat. #A1896701) medium supplemented with 10% FBS, 1% Pen-strep, and 1x GlutaMAX (Thermo Fisher Scientific, cat. #35050061). For time-course experiments, cells were stimulated with 1 µM Bafilomycin A1 (Santa Cruz Biotechnology cat. #sc-201550),<strong> </strong>1 µM diABZI (Invivogen, #tlrl-diabzi), 20 µg/mL cGAMP (Invivogen, #tlrl-nacga23-1) with 5 ng/µL digitonin (Promega, #G9441) for 1 hr with or without the addition of 10 µM C53 (Cayman, #37354). All images were acquired using a Ti2-E inverted epifluorescence microscope (Nikon) with automated XYZ stage control, hardware autofocus, and a Yokogawa CSU-W1 confocal spinning disk unit with Zyla 4.2 PLUS sCMOS camera. An Okolab cage incubator was set to 37°C with 5% CO2. 405, 488, 561, and 640 nm laser lines were used for fluorescence illumination and all hardware was controlled using NIS elements software. Images were acquired using a 40X 0.95 NA CFI Plan Apo λ objective (Nikon MRD70470) with the following lasers and filters: Hoechst (405 nm laser, Chroma Multi LED set #89401), superecliptic pHluorin (488 nm laser, Chroma Multi LED set #89401), and mRuby3 (561 nm laser, Chroma Multi LED set #89401), assaying three z planes per field of view with 1.25 µm spacing. Fields of view were selected using NIS Elements software coordinates without manual preselection.</p> <p>Images are maximum projections of multiple z-stacks with each frame representing one timepoint: 0, 10, 20, 30, 40, 50, 60 minutes post treatment. Channels are: Hoechst 34580, SEP (super-ecliptic pHluorin), mRuby3, and SEP/mRuby3 (ratio). Crops indicate cropped fields of view presented in the manuscript.</p>
Human STING is a proton channel (Live-cell MGAT pH Measurement upon STING agonist treatment with or without C53)
<p>hTERT-immortalized BJ1 cells (ATCC CRL-2522) were transduced with lentiviral ratiometric reporters targeted to MGAT constructed based on designs reported in Linders et al. <em>ACS Chem. Biol. </em>2022, with superecliptic pHluorin and mRuby3. Transduced cells were sorted based on mRuby3 expression using a Sony MA900 sorter. BJ1 SEP-mRuby3 cells were plated in 24-well glass-bottom plates (Greiner Bio-One) at 40,000 cells/well. After 48 hours, cells were stained for 45 minutes at 37°C with 0.5 µg/ml Hoechst 34580 (Thermo Fisher Scientific, cat. #H21486). Cells were then washed and incubated in Fluorobrite DMEM (Thermo Fisher Scientific, cat. #A1896701) medium supplemented with 10% FBS, 1% Pen-strep, and 1x GlutaMAX (Thermo Fisher Scientific, cat. #35050061). For time-course experiments, cells were stimulated with 1 µM Bafilomycin A1 (Santa Cruz Biotechnology cat. #sc-201550),<strong> </strong>1 µM diABZI (Invivogen, #tlrl-diabzi), 20 µg/mL cGAMP (Invivogen, #tlrl-nacga23-1) with 5 ng/µL digitonin (Promega, #G9441) for 1 hr with or without the addition of 10 µM C53 (Cayman, #37354). All images were acquired using a Ti2-E inverted epifluorescence microscope (Nikon) with automated XYZ stage control, hardware autofocus, and a Yokogawa CSU-W1 confocal spinning disk unit with Zyla 4.2 PLUS sCMOS camera. An Okolab cage incubator was set to 37°C with 5% CO2. 405, 488, 561, and 640 nm laser lines were used for fluorescence illumination and all hardware was controlled using NIS elements software. Images were acquired using a 40X 0.95 NA CFI Plan Apo λ objective (Nikon MRD70470) with the following lasers and filters: Hoechst (405 nm laser, Chroma Multi LED set #89401), superecliptic pHluorin (488 nm laser, Chroma Multi LED set #89401), and mRuby3 (561 nm laser, Chroma Multi LED set #89401), assaying three z planes per field of view with 1.25 µm spacing. Fields of view were selected using NIS Elements software coordinates without manual preselection.</p> <p>Images are maximum projections of multiple z-stacks with each frame representing one timepoint: 0, 10, 20, 30, 40, 50, 60 minutes post treatment. Channels are: Hoechst 34580, SEP (super-ecliptic pHluorin), mRuby3, and SEP/mRuby3 (ratio). Crops indicate cropped fields of view presented in the manuscript.</p>
Human STING is a proton channel (Live-cell MGAT STING WT or S53L pH Measurement upon STING agonist treatment with or without C53)
<p>hTERT-immortalized BJ1 cells (ATCC CRL-2522) were transduced with lentiviral ratiometric reporters targeted to MGAT constructed based on designs reported in Linders et al. <em>ACS Chem. Biol. </em>2022, with superecliptic pHluorin and mRuby3. Transduced cells were sorted based on mRuby3 expression using a Sony MA900 sorter. Cells then were transduced with pXPR023 (lentiCRISPRv2) expressing an sgRNA targeting STING and selected with 0.1 µg/mL puromycin for 5 days. Finally, cells were transduced with blasticidin-STING-HA (WT or S53L) and selected using 10 µg/mL blasticidin HCl for 5 days.<strong> </strong> BJ1 SEP-mRuby3 STING-HA (WT or S53L) cells were plated in 24-well glass-bottom plates (Greiner Bio-One) at 40,000 cells/well. After 48 hours, cells were stained for 45 minutes at 37°C with 0.5 µg/ml Hoechst 34580 (Thermo Fisher Scientific, cat. #H21486). Cells were then washed and incubated in Fluorobrite DMEM (Thermo Fisher Scientific, cat. #A1896701) medium supplemented with 10% FBS, 1% Pen-strep, and 1x GlutaMAX (Thermo Fisher Scientific, cat. #35050061). For time-course experiments, cells were stimulated with 1 µM diABZI (Invivogen, #tlrl-diabzi) for 1 hr with or without the addition of 10 µM C53 (Cayman, #37354). All images were acquired using a Ti2-E inverted epifluorescence microscope (Nikon) with automated XYZ stage control, hardware autofocus, and a Yokogawa CSU-W1 confocal spinning disk unit with Zyla 4.2 PLUS sCMOS camera. An Okolab cage incubator was set to 37°C with 5% CO2. 405, 488, 561, and 640 nm laser lines were used for fluorescence illumination and all hardware was controlled using NIS elements software. Images were acquired using a 40X 0.95 NA CFI Plan Apo λ objective (Nikon MRD70470) with the following lasers and filters: Hoechst (405 nm laser, Chroma Multi LED set #89401), superecliptic pHluorin (488 nm laser, Chroma Multi LED set #89401), and mRuby3 (561 nm laser, Chroma Multi LED set #89401), assaying three z planes per field of view with 1.25 µm spacing. Fields of view were selected using NIS Elements software coordinates without manual preselection.</p> <p>Images are maximum projections of multiple z-stacks with each frame representing one timepoint: 0, 10, 20, 30, 40, 50, 60 minutes post treatment. Channels are: Hoechst 34580, SEP (super-ecliptic pHluorin), mRuby3, and SEP/mRuby3 (ratio). Crops indicate cropped fields of view presented in the manuscript.</p>
Human STING is a proton channel (HEK293T Autophagy Experiment)
<p>RFP-LC3 and STING-HA-expressing FIP200 KO 293T cells were seeded on Fibronectin bovine plasma coated 24-well glass-bottom plates (Greiner Bio-One) the night before stimulation. Cells were then stimulated with 20 µg/ml cGAMP (Invivogen, #tlrl-nacga23-1) with 5ug/ml digitonin (Promega, #G9441) or 1 µM DIABZI (Invivogen, #tlrl-diabzi) with or without the addition of 10 µM C53 (Cayman, #37354) for 1 hour. Cells were then fixed with 2% Paraformaldehyde (Electron Microscopy Sciences) in PHEM buffer (Electron Microscopy Sciences) for 30 minutes at 37°C, washed three times with PBS and quenched with freshly prepared 0.1M Glycine for 10 minutes. Cells were permeabilized in 100% methanol for 30 minutes and stained with anti-HA (Millipore, #11867423001) for 1 hour at room temperature in 3% BSA, washed 5 times, and then stained with Alexa 647 anti-rat IgG (H+L) (Thermo, A-21247) in 3% BSA for 1 hour. After five washes, cells were incubated in 2X SSC with 200 ng/mL DAPI (Thermo Fisher) and imaged using the Nikon microscope used for organelle pH images. Images were acquired using a 60X 1.40 NA Plan Apo λ oil immersion objective (Nikon MRD01605) with Nikon type F immersion oil with the following lasers and filters: DAPI (405 nm laser, Chroma <a href="https://www.chroma.com/products/parts/et455-50m">ET455/50</a>), RFP-LC3B (561 nm laser, Chroma ET605/52), and STING-HA (640 nm laser, Chroma ET705/72), assaying five z planes per field of view with 0.625 µm spacing. Fields of view were selected using NIS Elements software coordinates without manual preselection.</p> <p>Images are maximum projections of multiple z-stacks. Channels are: DAPI, LC3B-RFP, and STING.</p>
Human STING is a proton channel (Live-cell pH Calibration Meaurements)
<p>hTERT-immortalized BJ1 cells (ATCC CRL-2522) were transduced with lentiviral ratiometric reporters targeted to GALT constructed based on designs reported in Linders et al. <em>ACS Chem. Biol. </em>2022, with superecliptic pHluorin and mRuby3. Transduced cells were sorted based on mRuby3 expression using a Sony MA900 sorter. BJ1 SEP-mRuby3 cells were plated in 24-well glass-bottom plates (Greiner Bio-One) at 40,000 cells/well. After 48 hours, cells were stained for 45 minutes at 37°C with 0.5 µg/ml Hoechst 34580 (Thermo Fisher Scientific, cat. #H21486). Cells were then washed and incubated in Fluorobrite DMEM (Thermo Fisher Scientific, cat. #A1896701) medium supplemented with 10% FBS, 1% Pen-strep, and 1x GlutaMAX (Thermo Fisher Scientific, cat. #35050061). For pH calibration experiments, cells were treated with buffers at defined pH values supplemented with nigericin and valinomycin following manufacturer’s instructions (Thermo Fisher Scientific cat. # P35379). Additional buffers at pH 7, 6, and 5 were created by titration with acid. All images were acquired using a Ti2-E inverted epifluorescence microscope (Nikon) with automated XYZ stage control, hardware autofocus, and a Yokogawa CSU-W1 confocal spinning disk unit with Zyla 4.2 PLUS sCMOS camera. An Okolab cage incubator was set to 37°C with 5% CO2. 405, 488, 561, and 640 nm laser lines were used for fluorescence illumination and all hardware was controlled using NIS elements software. Images were acquired using a 40X 0.95 NA CFI Plan Apo λ objective (Nikon MRD70470) with the following lasers and filters: Hoechst (405 nm laser, Chroma Multi LED set #89401), superecliptic pHluorin (488 nm laser, Chroma Multi LED set #89401), and mRuby3 (561 nm laser, Chroma Multi LED set #89401), assaying three z planes per field of view with 1.25 µm spacing. Fields of view were selected using NIS Elements software coordinates without manual preselection.</p> <p>Images are maximum projections of multiple z-stacks with each frame representing one pH value: 7.5, 7, 6.5, 6, 5.5, 5, and 4.5 (except for replicate 1, which omitted pH 7). Channels are: Hoechst 34580, SEP (super-ecliptic GFP), mRuby3, and SEP/mRuby3 (ratio). Crops indicate cropped fields of view presented in the manuscript.</p>
Human STING is a proton channel (Live-cell MGAT, GALT, and LAMP1 pH Measurements Upon BafA1 and diABZI treatment)
<p>hTERT-immortalized BJ1 cells (ATCC CRL-2522) were transduced with lentiviral ratiometric reporters targeted to MGAT, GALT, or LAMP1 constructed based on designs reported in Linders et al. <em>ACS Chem. Biol. </em>2022, with superecliptic pHluorin and mRuby3. Transduced cells were sorted based on mRuby3 expression using a Sony MA900 sorter. BJ1 SEP-mRuby3 cells were plated in 24-well glass-bottom plates (Greiner Bio-One) at 40,000 cells/well. After 48 hours, cells were stained for 45 minutes at 37°C with 0.5 µg/ml Hoechst 34580 (Thermo Fisher Scientific, cat. #H21486). Cells were then washed and incubated in Fluorobrite DMEM (Thermo Fisher Scientific, cat. #A1896701) medium supplemented with 10% FBS, 1% Pen-strep, and 1x GlutaMAX (Thermo Fisher Scientific, cat. #35050061). For time-course experiments, cells were stimulated with 1 µM Bafilomycin A1 (Santa Cruz Biotechnology cat. #sc-201550), or 1 µM diABZI (Invivogen, #tlrl-diabzi). All images were acquired using a Ti2-E inverted epifluorescence microscope (Nikon) with automated XYZ stage control, hardware autofocus, and a Yokogawa CSU-W1 confocal spinning disk unit with Zyla 4.2 PLUS sCMOS camera. An Okolab cage incubator was set to 37°C with 5% CO2. 405, 488, 561, and 640 nm laser lines were used for fluorescence illumination and all hardware was controlled using NIS elements software. Images were acquired using a 40X 0.95 NA CFI Plan Apo λ objective (Nikon MRD70470) with the following lasers and filters: Hoechst (405 nm laser, Chroma Multi LED set #89401), superecliptic pHluorin (488 nm laser, Chroma Multi LED set #89401), and mRuby3 (561 nm laser, Chroma Multi LED set #89401), assaying three z planes per field of view with 1.25 µm spacing. Fields of view were selected using NIS Elements software coordinates without manual preselection.</p> <p>Images are maximum projections of multiple z-stacks with each frame representing one timepoint: 0, 10, 20, 30, 40, 50, 60 minutes post treatment (except for replicate 1, which omitted the final timepoint). Channels are: Hoechst 34580, SEP (super-ecliptic pHluorin), mRuby3, and SEP/mRuby3 (ratio). Crops indicate cropped fields of view presented in the manuscript.</p>
Human STING is a proton channel (HEK293T Inflammasome Experiment)
<p>HEK293T cells transduced to express NLRP3-mNeonGreen and STING-HA were plated in 24-well glass-bottom plates (Greiner Bio-One) and, after 24 hours, stimulated with 2 µM nigericin or 1 µM diABZI with or without the addition of 10 µM C53 for 1 hour. Cells were then fixed with 2% Paraformaldehyde (Electron Microscopy Sciences) in PHEM buffer (Electron Microscopy Sciences) for 30 minutes at 37°C, washed three times with PBS and quenched with freshly prepared 0.1M Glycine for 10 minutes. Cells were permeabilized in 100% methanol for 30 minutes and stained with anti-HA (Millipore, #11867423001) and anti p-STING (Cell Signaling Technology cat. #19781s) for 1 hour at room temperature in 3% BSA, washed 5 times, and then stained with Alexa 647 anti-rat IgG (H+L) (Thermo, A-21247) and Alexa 555 plus anti-rabbit (Thermo, A32732) in 3% BSA for 1 hour. After five washes, cells were incubated in 2X SSC with 200 ng/mL DAPI (Thermo Fisher) and imaged using the Nikon microscope used for organelle pH images. Images were acquired using a 60X 1.40 NA Plan Apo λ oil immersion objective (Nikon MRD01605) with Nikon type F immersion oil with the following lasers and filters: DAPI (405 nm laser, Chroma <a href="https://www.chroma.com/products/parts/et455-50m">ET455/50</a>), NLRP3 mNeonGreen (488nm laser, Chroma ET525/36) pSTING (561 nm laser, Chroma ET605/52), and STING-HA (640 nm laser, Chroma ET705/72), assaying five z planes per field of view with 0.625 µm spacing. Fields of view were selected using NIS Elements software coordinates without manual preselection.</p> <p>Images are maximum projections of multiple z-stacks. Channels are: DAPI, NLRP3 mNeonGreen, pSTING, and STING.</p>
KScale Tropical Channel 2.2 km resolution Precip
<p>KScale Tropical channel 2.2 km resolution precipitation data. Model run initialised 20171230T0600Z and running from T+0 to T+288 (12 days)</p>
Channel flow with hydrodynamically controlled benthic-pelagic coupled oxygen fluxes
<p>This dataset was used for the manuscript "Hydrodynamic control of sediment-water fluxes: Consistent parameterization and impact in coupled benthic-pelagic models" by Umlauf et al. (2023, JGR Oceans, <a href="https://doi.org/10.1029/2023JC019651" target="_blank" rel="noopener">10.1029/2023JC019651</a>).</p>
Raw data for: Crosstalk between regulatory elements in the disordered TRPV4 N-terminus modulates lipid-dependent channel activity
<p>This repository contains raw data and code related to "Crosstalk between regulatory elements in the disordered TRPV4 N-terminus modulates lipid-dependent channel activity" by Goretzki et al.</p> <p>Included are molecular dynamics parameter files, initial structures after system equilibration, production trajectories, and final structures of simulations of:<br> 1. coarse-grained IDRs on membrane, and force and position data for restrained c-termini. Trajectories are subsampled with one frame every 50 ns.<br> 2. The tetrameric TRPV4 core in a POPC in atomistic resolution. Trajectories are sampled with one frame every 1 ns. <br> 3. The isolated ARD in solution in atomistic resolution. Trajectories are subsampled with one frame every 1 ns.</p> <p>Contact information:<br> Name: Stefan L. Schaefer<br> Institution: Department of Theoretical Biophysics, Max Planck Institute of Biophysics<br> Address: Max-von-Laue-Str. 3, 60438 Frankfurt am Main, Germany<br> Email: stefan.schaefer@biophys.mpg.de</p> <p>Name: Ainara Claveras Cabezudo<br> Institution: Department of Theoretical Biophysics, Max Planck Institute of Biophysics<br> Address: Max-von-Laue-Str. 3, 60438 Frankfurt am Main, Germany<br> Email: ainara.claveras@biophys.mpg.de</p>
Kirchhoff pre-stack depth migration images of the multi-channel seismic data, SO190, RV. SONNE
<p>The dataset consists of four newly processed 2-D pre-stack depth migrated multi-channel seismic lines (BGR06_303, BGR06_305, BGR06_311 and BGR06_313) collected by GEOMAR and BGR in 2006. The dataset reveals the subducted oceanic reliefs and detailed accretionary wedge structure offshore eastern Java, Bali, Lombok, and Sumbawa islands, along the Sunda arc. The dataset is saved in standard SEGY format and could be loaded in open-source or commercial software. </p>
Dataset of stereo and multi-channel IRs for a 50-point Lebedev quadrature.
<p>We present a free dataset of Impulse Response measurements for all positions on a 50-point Lebedev arranged loudspeaker array for a variety of stereo microphone configurations, 32 Eigenmic capsules, and up to 4th Order Ambisonics. This dataset has particular relevance for those interested in training novel stereo to ambisonic upmix algorithms. </p>
A 12-years long (2010-2021) hydrological and biogeochemical dataset in the Sicily Channel (Mediterranean Sea)
<p>The data set presented here consists of 273 CTD-nutrient stations and 2034 data points collected in 12 summer oceanographic cruises, called BANSIC, carried out in the Strait of Sicily, Mediterranean Sea (11.304-15.3203°W; 35.50383-37.732°N) between 2010 and 2021. At all stations, pressure, salinity, and temperature were measured with a CTD (conductivity, temperature, and depth) probe consisting of a CTD SBE 911plus and a General Oceanics rosette with 24 Niskin bottles of 12 L capacity. Seawater samples for dissolved inorganic nutrient analysis were collected from the surface to the bottom by means of Niskin bottles. In particular, during the CTD upcast, a variable number of fixed depths has been considered (surface–25m–50m–75m–100m–150m-200m–300m–400m–500m–600m–700m–800m–900m–1000m–bottom) with slight modifications in the upper layer where significative hydrological variability was detected. An appropriate quality check has been carried out in order to ensure the reliability of the data made available to the scientific community. Data are described in the description paper Placenti et al., 2024, https://doi.org/10.5194/essd-16-743-2024.</p>
Investigation on Dynamic Characteristics of Lightning Return Stroke Channel
<p>The dynamic characteristics in lightning discharge plasma channel are of great significance in studying the micro-physical mechanism of the discharge process. This paper established a simplified radiation-hydrodynamic model (SRHM) of the return stroke channel radial expansion based on the fluid dynamics theory and the time evolution characteristics of the light radiation power observed by experiments. The influence of current waveform on the dynamic characteristics of return stroke channel was investigated, and the temporal evolutions of the characteristic parameters, such as temperature, pressure and expansion speed for return stroke channel were analyzed. The results indicated that the current peak value and the risetime are important factors in determining the channel dynamics characteristics. At the initial stage of return stroke, the light radiation loss has a distinct influence on channel temperature, which leads to a transitory drop in temperature forming a bimodal waveform structure. Following the peak current, the channel reaches peak pressure, which leads to a subsequent secondary temperature peak and accelerates the expansion of the channel. Large peak current and the rise time are the indicative parameters of strong discharge and the main factors leading to lightning disaster. This work provides reference data for further research on the radial energy transport of lightning return stroke channel and the formation mechanism of shock waves.</p>
Light-induced nanoscale deformation in azobenzene thin film triggers rapid intracellular Ca2+ increase via mechanosensitive cation channels
<p>This dataset contains raw data for a research article: material characterization data of Disperse Red 1 glass, calcium imaging data of Madin Darby Canine Kidney II epithelial cells that express the genetic calcium indicator jRCaMP1b and immunofluorescence stainings of Piezo1-channels and the actin cytoskeleton in the same cell line.</p> <p>Light induced material deformations were conducted with Zeiss LSM 780 confocal microscope with 488 nm wavelength excitation. The generated topographies were analyzed with atomic force microscopy (AFM) and digital holographic microscopy (DHM), and particle image velocimetry (PIV) was used to determine lateral deformations.</p> <p>Calcium imaging was conducted with the same microscope with 561 nm excitation and calcium signals were recorded in response to light induced material deformations (stimulation performed after 10 frames) (Zeiss C Apo 63x/1.20 objective, pixel size 200 nm, frame rate 1.23 sec/fame, channel1: fluorescence emission, channel2: brightfield). Apical stimulations were conducted with Nikon Eclipse FN1 utilizing micromanipulation (pixel size 200 nm, NIR Apo 40x 0.8W DIC N2 objective). Immunofluorescence stainings (in normal conditions (channel1: nuclei, channel2: Piezo1, channel3: jRCaMP1b, channel4: actin) or after cytochalainD treatment showing actin cytoskeleton depolymerization (channel1: nuclei, channel2: ZO1, channel3: jRCaMP1b, channel4: actin)) were imaged with Nikon A1R (SR Apo TIRF 100x/1.49 objective, pixel size 40 nm, Z-step to 99 nm, deconvolution with Huygens Essential)</p>
Datasets that simulated ion channel currents
<p>This repository contains pseudo-ion-channel current datasets described in the 2023 publication “Model-Free Idealization: Adaptive Integrated Approach for Idealization of Ion Channel Currents (AI2)”. The datasets simulate ion channel currents based on the two-state model (Gating Kinetics.tif) and contain two kinds of noise (experimental or white Gaussian noise) at different signal-to-noise ratios (SNRs=10.2, 5.14, and 1.82). Four values (1, 10, 100, and 1000 s<sup>-1</sup> ) were examined for k<sub>1</sub> and k<sub>2</sub> of the gating kinetics, yielding 16 combinations of k<sub>1</sub> and k<sub>2</sub> . The repository contains five time-series data for each combination of k<sub>1</sub> , k<sub>2</sub> , and SNR. Each dataset contains 5×10<sup>5</sup> points which correspond to a 20 s recording with a sampling frequency of 25 kHz.</p> <p><br> Time-series 0-1 (closed-open) sequences were first simulated using the QuB software. White Gaussian noise was added to the 0-1 sequence by Python 3.7. Experimental noise was added to the 0-1 sequence through electrophysiological recordings using a patch-clamp amplifier and a model cell (Molecular Devices). Voltage sequences consisting of V<sub>0</sub> and V<sub>1</sub> , which corresponded to the closed and open states, respectively, were input to the model cell (10 MΩ resister), and the resulting currents were recorded with the amplifier. Each CSV file has time, ground truth (0 or 1), and current.</p>
Structure of human TRPM8 channel
<p>This repository includes the following source datasets:</p> <p><strong>1. modeling.zip</strong><br> Modeling of icilin binding to HsTRPM8 (Figure 3e, 3f, 3g, 3h)<br> - HsTRPM8-KX7_opt.pdb: original pose (Figure 3e, 3f)<br> - HsTRPM8-KX7_opt_rotated.pdb: rotates pose (Figure 3g, 3h)</p> <p><strong>2. activation_assay.zip</strong><br> HsTRPM8 activation assay results (Figure 3i and Supplementary Figure 5)<br> - HsTRPM8_activation_assay_results.pzf: GraphPad file with activation Assay results</p> <p><strong>3. Fr-TM.zip</strong><br> Structure-based multiple sequence alignment of TRPM channels (Supplementary Figure 4a)<br> - Fr-TM_info.txt: description of procedure used to create alignment<br> - TRPM_new_raw_pairwise_alignments.fas: raw pairwise alignment of new TRPM sequences to 6CO7 reference<br> - TRPM_S6_restriction_site_aligned.fas: final multiple sequence alignment used to generate Supplementary Figure 4a</p> <p><strong>4. 3Dvar.zip</strong><br> HsTRPM8 3D Variability Analysis results (Supplementary Movie 1)<br> - *.mrc files: composite maps with extreme frames for two analyzed components (aligned with focused MHR1/2 map)<br> - *.pdb files: HsTRPM8 models fitted (MDFF) to above maps and used to generate Supplementary Movie 1</p> <p><strong>5. Supplementary_Movie_1.mp4</strong><br> Morphing between different conformations of HsTRPM8 resolved by 3D Variability analysis (Supplementary Movie 1).</p>
Patterns of Alluviation in Mixed Bedrock-Alluvial Channels
<p><strong>morph2d</strong></p> <p>Filename: morph2D.f90<br> 2-Dimensional Morphodynamic Model<br> Written by Jongseok Cho and Peter A. Nelson<br> Department of Civil and Environmental Engineering<br> Colorado State University, Fort Collins, Colorado<br> <br> Filename: P1505.mat<br> Results from the simulation of bar formation in a straight flume.<br> <br> Filename: BRtopo.txt<br> Randomly abraded bedrock topography is used to simulate the mixed bedrock-alluvial channels.<br> <br> Filename: XYZ.mat<br> The x- and y-coordinates and bedrock elevation are used in the simulations of mixed bedrock-alluvial channels.<br> <br> Filename: 2-Ax.mat, 2-Bx.mat, and 2-Dx.mat<br> Time evolution of alluvial thickness and the fraction of exposed bedrock surface for the simulations starting from the bare bedrock bed channel.<br> <br> Filename: 2-A.mat and 2-B.mat<br> Time evolution of alluvial thickness and the fraction of exposed bedrock surface for the simulations starting from the alluvial bed channel.<br> <br> Filename: 2-B2-z.mat<br> Time evolution of alluvial thickness and the fraction of exposed bedrock surface for the simulations starting from the alluvial bed channel with different sediment layer thickness.<br> <br> Filename: 2-B2-k.mat<br> Time evolution of total, bed surface, sediment transport, and bedform roughnesses for the simulations starting from the alluvial bed channel with different sediment layer thickness.<br> <br> Filename: 2-B2-x.mat<br> Time evolution of alluvial thickness and the fraction of exposed bedrock surface for the simulations starting from the alluvial bed channel without the effects of bedform and sediment transport roughnesses and shear stress correction for bedload transport.</p>
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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.