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Seahorse Analytics provides a wide variety of bar chart options to add to an analysis view, and many are assay specific. For more information about specific bar chart widgets please refer to the specific assay kit companion analysis view here or in Seahorse Analytics. For example, to show OCR data from rate measurement 10 for all groups:. On the widget editor view, use the Rate drop-down menu to select rate measurement 10, then click the back arrow upper-left corner of the widget editor view to return to the analysis view.
In addition to the Energy Map widget described below, there are several additional scatter plot widget options you can add to your analysis views that are assay type dependent and defined in the Analysis Views section. Energetic Map Basal. Please also note that buffer factor must be properly assigned to the assay media, background wells, and assay groups to calculate this widget data. Calculations used for this widget can be found in the details on the Add Widget dialog pictured right.
For XF ATP Rate assays with more than 2 injections, you must identify the oligomycin injection using the drop-down menu seen on the Add Widget pictured right before you can add this widget to your analysis view. This oligomycin injection selection plays a critical role in calculating the correct Basal ATP production rates that you will see on the widget.
Incorrect selection of the oligomycin injection will result in incorrect calculations and data. Energetic Map Induced. Please also note that buffer factor must be properly assigned to the assay media, background wells, and assay groups before you can calculate this widget data. Calculations used for this widget can be found in the details on the Add Widget dialog pictured below, right. The oligomycin injection selection plays a critical role in calculating the correct induced ATP production rates that you will see on the widget.
XF Cell Energy Phenotype. This is a unique widget compared to the other scatter plot widget options in Seahorse Analytics as it plots 2 data points per group — the baseline phenotype and the stressed phenotype, connected by a dashed line called the metabolic potential — and the y-axis is always OCR and the x-axis is always ECAR pictured below. This widget applies to both the standard and induced assay workflows. The ATP Production Rate Induced widget creates a stacked bar chart of the average of the induced glycoATP production rates upper blue bar and the average of the induced mitoATP production rates bottom red bar for each group pictured below, right.
This widget applies to the induced assay workflow only. The XF ATP Rate Index widget plots the ratio of basal mitoATP production rate to basal glycoATP production rate as an empty circle marker, and plots the ratio of the average of the induced mitoATP production rates to the average of the induced glycoATP production rates for each group as a filled circle marker only when applied to an induced assay result file — widget pictured below shows data from an induced XF ATP rate assay.
Export your data to a Microsoft Excel or GraphPad Prism file or share your result data and insight with a collaborator directly using Seahorse Analytics. You can create an Excel and Prism file containing all rate data for the selected file. This export will not include any parameter calculations i. Spare Respiratory Capacity that you have calculated in an analysis view, you will need to export that data individually from each widget.
How is this export feature used? This type of data export allows users to easily transfer all rate data for OCR, ECAR, and PER data into Prism or Excel to create high-quality or customized figures, perform statistical analysis, and other analytical functions not offered in Seahorse Analytics. Export select data from a widget. You can export individual widget data to an Excel and Prism file containing data for the selected widget.
The data in the export file will match exactly how you formatted the widget. For example, if you configure a widget to display basal respiration in well mode, the Prism export file will contain individual well values for basal respiration data for each group. If you configure a widget to display basal respiration in group mode, the Prism export file will show the average group value and error value, not individual well values.
This type of data export allows users to easily export select rate or parameter data as an image file, or as a Prism or Excel file. The Prism and Excel export allow you to get exactly the data you want to further analyze i. You can share individual assay result files with collaborators or your team using the built-in file share feature. The share feature is found under the small 3-dot menu to the right of each assay result file on the Home and Files views pictured right.
If the recipient does not have a Seahorse Analytics account, they must create one to view the data file. If the recipient has an account, they will receive an email notifying them a file was shared with them.
They will also see a notification in Seahorse Analytics bell icon in the upper-right corner where they will accept or reject the shared file. How is this sharing feature used? The share feature allows you to send an assay result file to someone with, or without, a Seahorse Analytics account directly through the application. The recipient can make modifications to the shared file, but your copy of the file will remain unchanged.
Transform complex cellular metabolism data into publishable results using Wave Desktop's flexible analysis views, embedded reporting tools, and other powerful analytical capabilities. It is always encouraged to update to the latest version of Wave Desktop software. The latest release of Wave Desktop software is version 2. Below you will find the PC specs and compatibility detail for Wave Desktop 2.
Cellular oxygen consumption respiration and proton excretion glycolysis cause rapid, easily measurable changes to the concentrations of dissolved oxygen and free protons. Only available in post-run assay results, not during assay runtime. See chapter 3 in the Wave User Guide for more information about the types of data available in Wave software.
Oxygen Concentration mmHg : As cells or other biological material consumes oxygen during a measurement, oxygen tension will decrease.
This decrease in oxygen tension is used to calculate the rate of oxygen consumption OCR. You can view oxygen tension level data on the Overview analysis view using the Y1 drop-down menu. Oxygen tension O 2 data displayed as mmHg vs. Proton Concentration mpH : As cells or other biological material generate protons during a measurement, proton concentration will increase.
The concentration of free protons in the microchamber is measured throughout an XF assay and calculated as the rate of extracellular acidification ECAR. You can view mpH level data on the Overview analysis view using the Y1 drop-down menu. Proton Concentration mpH data displayed in Level mode right. Depending on the type of analysis view selected, Wave automatically calculates and graphs result data as one of the following:.
A kinetic graph displays the rate on the y-axis, and time on the x-axis. During an assay, data is acquired and plotted in real-time as a kinetic graph. Kinetic graphs can be found in the Quick View and Overview analysis views in Wave software.
Use the Measurement drop-down menu to select a rate measurement to display on the energy map for each group. Use the Rate drop-down menu to change the x-axis rate to PER. ECAR analysis views. The Plate Map displays rate data for the selected rate measurement of each assay well. The Quick View has a button to display the Plate Map, which is hidden by default.
When opening a new analysis view, the Plate Map shows data for rate measurement 1 by default. Use the Rate drop-down menu to display data for another rate measurement during the assay. The Bar Graph is available on the Overview analysis view only below the Plate Map , and displays the average rate for each group for the selected measurement.
Use the Display drop-down menu to change the rate display from Group average to Well individual well mode. The Bar Graph can be used for identifying outliers, optimal FCCP concentration, optimal cell seeding density, or other trends that may not be apparent when measurement data is plotted as a kinetic graph or scatter plot.
The Group List is the legend for the data plotted in the kinetic graph or scatter plot. There are 4 customizable analysis views that can be added to an assay result file in Wave Desktop. Each analysis view can be added to an assay result file multiple times using the Add View button in the top-level ribbon menu.
Quick View is the default analysis view displayed when opening a new assay result file. The selected rate is displayed on the y-axis, and time is displayed on the x-axis. Group statistics average rate and error for each measurement can be displayed by checking the Details box in the Group List below the kinetic graph.
Overview is the most versatile analysis view in Wave software for routine analysis functions. To display Overview , click Add View and select Overview from the list of views. This gives greater flexibility for tailoring your result data presentation to show specific groups, responses, or comparisons between groups. The OCR vs. OCR is always displayed on the y-axis, and cannot be changed.
To display OCR vs. ECAR from the list of views. The Data view contains all data associated with the assay result file organized into 7 tabs:. To display the Data view, click Add View and select Data from the list of views. The Group Data tab is displayed by default when opening the Data view. Click the Export button in the top-level ribbon menu to display the list of available XF Report Generator export options. This section of the XF Learning Center will provide an introduction to various topics on using XF Analyzers, including a range XF assay kits and applications, alternative assay conditions and sample types, as well as normalization and analysis of XF data.
Agilent XF Assay Kits and reagents are developed specifically for use with each XF Analyzer to ensure reliability and consistency of results. Seahorse XF kits and reagents help simplify running an XF assay by providing pre-calibrated, pre-tested reagents for measuring valuable functional metabolic parameters including cellular ATP production rates, mitochondrial function, glycolytic activity and substrate oxidation in living cells, permeabilized cells and isolated mitochondria.
The materials below provide information and methods for performing a wide range XF Assays. Normalization of XF assays can be applied on several levels, including cell number, genomic DNA, and total cellular protein. The materials below provide information on methods for normalization of XF Data for your.
The regulation of metabolic pathways and energy expenditure, and how differential substrate oxidation contributes to metabolically regulated signaling mechanisms is an important topic for researchers in divers fields such as immunology, cancer and stem cell biology and drug target identification and mechanism-of-action studies. The study of mitochondrial function is central to both clinical and basic scientific research.
However, examining the precise enzyme or pathway driving observed changes can provide additional insight and further link-specific alterations in metabolic enzymes with disease states. A traditional method of studying substrate oxidation involves isolating mitochondria, and the XF Analyzers support a high-throughput assay in which both energy demand and substrate availability can be tightly controlled for mechanistic studies using minimal quantitiues of isolated mitochondria.
However, there are several disadvantages when isolating mitochondria, including limited quantity and a bias stemming from the sub-selection or damage of mitochondria during isolation.
XF Plasma Membrane Permeabilizer PMP forms pores in the plasma membrane of adherent cells without causing any concomitant damage to the mitochondrial membrane. This reagent overcomes the challenges associated with using isolated mitochondria or substrate-supplemented media with intact cells. Analyzers have the capability of measuring metabolism in reduced oxygen environments hypoxia , as well as with certain types of three-dimensional samples, including islets.
Analyzers have the capability of measuring metabolism in reduced oxygen environments hypoxia , as well as with certain types of three-dimensional samples, including spheroids. Analyzers have the capability of measuring metabolism in reduced oxygen environments hypoxia. Shop the online store to purchase cartridges, plates, kits, media, and reagents to your your XF assay.
Gather materials 1. Prepare for assay 2. Set up assay 3. Run assay 5. Analyze results W 5. Beyond the basics 6. Showing only information for the Seahorse Change instrument type.
Select a workflow step to display help content. Basic procedures for choosing cell seeding densities To effectively examine metabolic and bioenergetic function using your Agilent Seahorse Extracellular Flux Analyzer, it is essential to first characterize a specific cell type with respect to its metabolic activity under basal and maximal respiration OCR and extracellular acidification ECAR.
Experiment Rationale Accelerated Workflow Standard Workflow Seed cells at single or different densities and visually assess degree of cell confluence; choose a miniplate for the next step. Visual assessment is a good first approximation of optimal cell density and will be verified in each assay. Seed miniplates at different densities according to the diagram below. Seed 1 miniplate at a single cell density; hydrate 1 XFp cartridge. Choose cell densities to test, based on standard or accelerated workflow described above.
Remove a three-pack of miniplates from the blue box. Remove the foil seal from the tub s that will be used. Add sterile water or PBS to the moat around the cell culture wells. These are background correction wells.
Within the Cell Type group definition, click Cell Type and Add to add a new cell type entry and enter the name of cell type you intend to analyze in your assay. It is recommended to add the seeding density to group name. When designing your assay template, you can: Create a new assay template for the 3rd and 4th cell seeding density groups. Add 4 cell seeding density groups to one assay template and reassign the 3rd and 4th cell group to the plate map after performing the first assay with cell seeding density groups 1 and 2.
Rename groups in this template after performing the first assay with cell seeding density groups 1 and 2. Assign the first cell seeding density group to the plate map. To assign a group to the plate map, first click the group name in the group list, then: Click the column header i. A, B, C, etc. Click individual wells on the plate map. Repeat for the next cell seeding density group. Modifying the instrument protocol settings directly affects how data is acquired during your assay.
For this example, the default instrument protocol is used and recommended. Should you need to modify the default instrument protocol, prior to performing your cell seeding density optimization assay it is recommended to review the instrument protocol section in the Wave User Guide , or if necessary, contact Agilent Cell Analysis Technical Support.
Place the sensor cartridge upside down next to the utility plate. Remove and discard the water from the utility plate. Lower the sensor cartridge onto the utility plate, submerging the sensors in calibrant. Remove the assembled sensor cartridge with Hydro Booster and Utility plate from the incubator.
Remove and discard the Hydro Booster. A: image shows low end of optimal cell density, ideal seeding density and distribution. B: image shows high end of optimal seeding density, some cell clusters can be seen. Place row labels lettered A-H to the left. The triangular notch will be in the bottom left-hand corner. Place row labels lettered A-D to the left. Place well labels lettered A-H to the left.
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Click Download Private Key. There are few things more fun than personalizing or tricking out your vehicle. Any Work Environment. Note that this doesn't do it automatically, you have to explicitly call the generator to create a completion script. Works with macOS and linux if hterm-notify is installed.
It allows you to perform the following actions on. Its intended purpose is staged zsh startup. It works similarly to Turbo mode in zinit. Inspired by zsh-pyenv. Inspired by Artisan. It provides a key binding control-u that will replace the current or previous command line with the command you will want to run next. It is heavily inspired by emoji-cli. It also adds the default bash ls aliases and changes some aliases to avoid conflicts with other commands that exa does not replace.
Requires brew. Falls back to find and cat. Searches in the local tree of subdirectories for files. This plugin works as a Prezto zstyle configuration option. Shows datetime date unix command in your prompt.
Includes fzf tooling. Provides quite a few useful aliases and functions. The motivation to replace the default plugin stems from the fact that it comes with some inconsistencies that make a few popular commands rather unintuitive, so this plugin makes the aliases consistent. This is a command-line shell plugin for undoing git add.
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Speeds up and simplifies common commands like clean cache, setup upgrade, compile di and much more in Magento 2 on containers.
These functions are permanently available until you delete them. Requires n. Inspired by zsh-rbenv. Based on the Oh-My-Zsh npm plugin. Requires fzf and jq. It was highly inspired by this article about using oathtool for 2 step verification. Supports Elementary OS Freya. Doesn't touch your existing. Includes pipenv completions. Very oh-my-zsh centric, the generated plugins will need editing to work with other frameworks.
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As it makes use of the module command it is much more efficient than spack load. It automatically registers fonts and sets all necessary environment variables to run the t32 toolset.
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Works better with a unicode font. Includes decorators for status of last command run, user hostname, git status, working directory, whether running as root, whether background jobs are running, and other information. Includes git status. Includes git and mercurial status, current time and time the last command took decorations in the prompt.
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Requires powerline-compatible fonts and the git-prompt plugin. Requires a powerline-compatible terminal font. Works better with dark backgrounds. Pure is not clean, clean is not pure. Works with standard fonts. Includes node and git status decorations. Does not require special fonts. Has git and last command exit status decorations.
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Includes git status and working directory decorations. Includes directory, git status, and hostname decorations. Works best with a unicode font. Includes git status decorations, username and hostname abbreviations, virtual environment, current working directory, return status of last command and the time.
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Frank keeps to the facts and only tells you extra things when they are important. Includes git status integration. Includes many different status cars. Inspired by the gitsome theme. In particular the branch name, difference with remote branch, number of files staged or changed, etc.
Shows decorators for truncated current directory, hostname and git status. Includes both light and dark modes and detects system settings for that on macOS and Linux. Uncludes git status, user host, path and date decorators. Includes git status, current directory, root status decorations. Includes decorators for git status, time and current directory. Related to powerlevel9k. This theme was inspired by a keycap set called DSA Hana.
This pairs well with the hana atom theme. Shows root status, git status, current directory and user hostname decorations. It shows username, hostname, current directory and git status decorations.
Works with macOS out-of the box, includes git status decorations. Includes decorations for the current directory and git status. Includes git status information.
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