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397 protocols using clampfit

1

Electrophysiological and Ca2+ Dynamics Analysis of Cardiomyocytes

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The electrophysiological and MEA data were analyzed using Clampfit version 11.1.0.23 (Molecular Devices) and a custom-made OriginLab program (OriginLab 2018b, Northampton, USA). For the patch-clamp and MEA recordings, comparisons between cell lines were performed with the non-parametric Kruskal–Wallis test followed by Dunn’s post-hoc multiple comparisons test (GraphPad Prism Version 5.02, San Diego, CA, USA). The Ca2+ peak parameters were analyzed using Clampfit (Molecular Devices). In these analyses, the instantaneous frequency was calculated by converting each interevent interval into a frequency and subsequently averaging these frequencies. In addition, Ca2+ traces were analyzed by identifying the signals as normal or abnormal and categorizing the abnormalities into subgroups. Data obtained from WT CMs (04511.WT and 04602.WT) were pooled as their Ca2+ peak parameter values were similar. Statistical analyses of Ca2+ and qRT-PCR data were conducted using the SPSS software version 24 (SPSS, Chicago, IL, USA). Comparisons within cell lines (before and after drug administration) were performed with non-parametric Wilcoxon and comparisons among cell lines (cell line-to-cell line comparison) with non-parametric Kruskal–Wallis with Bonferroni correction. Statistical significance levels are indicated as “ns” (not significant), * P < 0.05, ** P < 0.01, or *** P < 0.001.
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2

GABA Receptor Kinetics Characterization

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Dose–response relationships
were described with standard Hill’s equation in the form: where [GABA] is the agonist
concentration, and nh is Hill’s
coefficient. The time course of the macroscopic desensitization was
fitted with a single exponential function (Clampfit, Molecular Devices,
US) as:
The current deactivation
time course after application of saturating GABA pulse was fitted
with a biexponential function:
FR10 and FR500 parameters
were calculated as: where Amax refers to the current amplitude [pA], and Ax refers to the current value [pA] after x ms after its peak.
The deactivation time constant was calculated
as: where
The rise time (RT)
was calculated with the function build in Clampfit
(Molecular Devices, US) as 10–90% of the macroscopic current
onset.
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3

Tracking Limb Movements during Running

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To track limb movements during running, we used DeepLabCut (version 2.1.5.2, Mathis et al., 2018 (link), see Figures 3,4). We manually labeled the positions of the head and the 4 paws from 50 frames of each video. We then used 95% of the labeled frames to train the network using a ResNet-50-based neural network with default parameters for three training iterations. We validated with two shuffles and found that the test error for trot experiments was: 3.33 pixels and the train error: 2.37 pixels (image size: 1344 × 301). Similarly, we trained the network for gallop condition using a ResNet-50-based neural network with default parameters for one training iteration. We validated with two shuffles and found that the test error was: 3.43 pixels and the train error: 2.43 pixels (image size: 1936 × 230). These networks were then used to analyze videos from similar experimental settings. X and Y coordinates from the head and the four limbs were then extracted and interpolated to 10 kHz to match the EMG recordings. The latter were exported from LabScribe to Clampfit (Molecular Devices), and both sets of signals were merged in a single file, before being processed offline in Clampfit.
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4

Quantitative Electrophysiological Analysis

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Data analysis and graphing were performed using Excel (Microsoft), Igor Pro (Wavemetrics), Prism (GraphPad), and Clampfit (Molecular Devices). In this study, n refers to the number of recordings (one cell per animal). P < 0.05 was regarded as statistically significant.
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5

Patch-Clamp Recording of Striatal Neurons

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We prepared coronal brain slices of the striatum (300 μm in thickness) with a Leica VT1200 vibratome. Slicing was made in ice-cold cutting solution, which contained (in mM): 1.2 NaH2PO4, 26 NaHCO3, 2.5 KCl, 0.5 CaCl2, 7 MgCl2, 11 D-glucose, 5 Na-ascorbate, 3 Na-pyruvate and 220 sucrose. The slices were recovered by incubation in artificial cerebrospinal fluid (ACSF) containing (in mM): 124 NaCl, 1.2 NaH2PO4, 26 NaHCO3, 5 KCl, 1.3 MgCl2, 2.5 CaCl2 and 11 D-glucose at 32 °C for 30 min and at room temperature for more than 1 hour. The pH value and osmolality of the cutting solution and ACSF were adjusted to pH 7.3–7.4 and 290–300 mOsm. The solutions were aerated with 95% O2/5% CO2. The slices were perfused with oxygenated ACSF in a recording chamber (~1 ml/min) at 26–28 °C. Whole-cell patch clamp recording was performed with recording pipettes (2.5–4 MΩ) filled with internal solution containing (in mM): 0.3 Na-GTP, 10 Na2-phosphocreatine, 20 KCl, 125 K-gluconate, 4 Mg-ATP, 0.5 EGTA, 10 HEPES, adjusted to pH 7.3–7.4 and 310 mOsm. Data were collected with pCLAMP and analyzed with clampfit (Molecular Devices). For optogenetic stimulation of axonal terminals, 2-ms blue light (473 nm) pulses were delivered by LED coupled with a 40X water objective.
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6

Entorhinal Cortex Seizure-Like Event Recording

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Horizontal slices (400 μm) were placed in an RC-27L dual perfusion recording chamber (Warner Instruments) perfused with oxygenated aCSF (2–3 mL/min) for 5 min before perfusion with oxygenated control artificial CSF (aCSF) composed of (in mM): 126 NaCl, 2.5 KCl, 0.5 CaCl2, 26 NaHCO3, 1.25 NaH2PO4, 2 MgCl2, 1.5 Na-pyruvate, and 10 glucose (equilibrated with 95% O2 and 5% CO2, or aCSF with reduce divalent cations (1.6 mM CaCl2 and 0.8 mM MgCl2) and 100 μM 4-aminopyridine (4-AP). aCSF filled electrodes (<1 MΩ resistance) were placed in layer III of the medial entorhinal cortex. Data were acquired at 10 kHz on a Multiclamp 700B amplifier (Molecular Devices) with Clampex 10 acquisition software (Molecular Devices). Recordings were analyzed on Clampfit (Molecular Devices) and traces were high-pass filtered at 1 Hz for event analysis. Seizure like events (SLEs) were defined as events exhibiting tonic-clonic discharges that had a duration of 10 s or longer. Late recurrent discharges (LRDs) were defined as periods of seizure activity with interictal durations of less than 20 s.16 (link),17 (link),48 (link)
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7

Statistical Analysis of Neurophysiological Data

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Data were analyzed using Clampfit (Molecular Devices) and Prism 7 (GraphPad). Statistical significance was evaluated by regression analysis, Student’s t-tests, and ANOVA with p < 0.05. Except where otherwise noted, values are reported as mean ± SEM.
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8

K-ATP Current Measurement in Patch Clamp

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Pipettes were made from soda lime glass microhematocrit tubes (Kimble) and had a resistance of 1–2 MΩ when filled with pipette solution. All recordings were made in symmetrical KINT solution ((mM) 140 KCl, 10 HEPES, 0.5 EGTA (pH 7.4 with KOH)). ATP (Sigma) was applied as indicated. Free Mg2+ was maintained at 0.5 mM by supplementing ATP-containing solutions with MgCl2 where necessary. Currents were recorded at −50 mV, sampled at 3 kHz, and filtered at 1 kHz using an Axopatch 1D and Digidata 1322 A (Molecular Devices). KATP current was calculated as the difference between the current in the absence of nucleotides and in the presence of a fully inhibiting concentration of 5 mM ATP. The data were analyzed using Clampfit (Molecular Devices) and Excel (Microsoft), and are presented as individual replicates in scatter plots, alongside mean ± SEM.
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9

Kinetic Analysis of Voltage Sensor Phosphatase

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Data are presented as mean ± SD except for the ΔF/F versus voltage relationship of Anap, for which data are presented as mean ± SEM. Data analyses were performed using Microsoft Excel 2016, PatchMaster, Clampfit (Molecular Devices), and Igor Pro software. Statistical tests were conducted using Microsoft Excel 2016 and R statistical software.
The phosphatase activity of VSP was taken as the rate constant, which was determined by fitting of a normalized Kir current decay with a single exponential function (21 (link)–23 (link, no link found)) (SI Appendix, Fig. S1 A and B). QOFF-V curves and F-V curves of G214C* mutants were fitted with the Boltzmann equation: Q(V)/Qmax or F(V)/Fmax = 1/{1 + exp[−(V − V1/2)/β]}, where β is the slope factor and V1/2 is the half-maximum potential at which Q(V) = Qmax/2 or F(V) = Fmax/2. β is expressed as β = kT/ze0, where k is the Boltzmann’s constant, T is the absolute temperature, z is the effective valence, and e0 is the elementary charge. In some mutants where the QOFF did not clearly saturate within the experimental voltage range, the fitting of QOFF-V curves was performed on the stipulation that 0 < Q(V) < 1.
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10

Xenopus Oocyte Expression of Ion Channels

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cRNAs were made from osm-9 cDNA (in vector pGEMHE, gift of Dr C. Bargmann, Rockefeller University), ocr-4 cDNA (gift of Dr Y. Kohara, National Institute of Genetics, Japan, transferred to pOX (ref. 50 (link)), iav cDNA (ref. 38 (link)) (gift of J. Kim lab, KRIBB, South Korea transferred into pCR4-TOPO), and nan cDNA (synthesized and purchased from GenScript, Piscataway, NJ, in pcDNA3.1) using mMessage Machine kits (Ambion, TX) and injected at ∼50 ng per oocyte. Oocyte preparation, injection and culture have been described49 (link)50 (link). cRNAs were injected individually and in the following combinations: osm-9+ocr-4, iav+nan. Recordings were made one to three days after injection at room temperature using standard two electrode voltage clamp techniques52 (link) in a solution containing (in mM): 98 Na+, 2 K+, 1 Mg2+, 1 Ca2+, 104 Cl, 5 HEPES (pH 7.5 with NaOH). All recordings were performed using a Dagan CA 1-B oocyte clamp (Dagan, MN) and Clampex (Molecular Devices, CA). Currents were analysed offline using Clampfit (Molecular Devices, CA). Statistics and curve fitting were performed using Origin (OriginLab, MA).
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