Overview of uploading data to Cytobank

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Create an experiment to upload the data 

Before uploading data, you must register a Cytobank account on the correct Cytobank server. 

In order to upload fresh data to the Cytobank platform, you must first create an experiment. This can be done from the Experiment Manager, which is where you land after logging in.

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A new experiment can also be created at any time from the Experiments menu in the Cytobank navigation bar.

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After clicking to create a new experiment, fill out the necessary metadata and click the Create experiment button. 

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After clicking to create the experiment, you can choose files to upload in multiple ways: 

  1. Drag and drop your files to the upload interface. 
  2. Click the Add files button to open up a file chooser to select files from your file system. 
  3. Click the Upload files using zip file button to choose a ZIP file of FCS files to upload.

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The Cytobank platform scans your uploaded files to ensure transfer fidelity and also determines whether they conform to specifications using our  File QC system. 

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Configure the new experiment setup 

After the files are done uploading, you will be navigated to the Set up new experiment page where you will be asked to adjust the scales, compensate the files, annotate Sample tags and review panel assignments.

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Walk through steps one to four to QC your data: 

1. Adjust your scales? Clicking this button points to the Scales window. Click on Learn more if you need more information about the scales in the Cytobank platform. Once you have adjusted the scales, close the window by clicking on the Close button or anywhere outside of the Scales window. To access the Scales window at any moment, click on the Scales menu in the Experiment navigation bar.

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2. Set the experiment compensation? The second step directs you to the Compensation Editor.  Scaling and compensation impact the results of machine learning algorithm analyses in addition to basic analyses. Read this article for further information on how to properly scale and compensate data on the Cytobank platform.

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Once you finished to set the compensations go back to the Set up experiment page clicking on the button in the Experiment navigation bar. You can edit the compensations at any time by clicking on the Compensation menu.

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3. Annotate your files with sample tags? The next step points you to the Sample tags menu. If you click on it a drop-down menu will appear. To annotate your files select Add experiment dimensions. You can tag the files with Clusters, Conditions, Doses, Individuals, Timepoints, or a custom dimension. You can also do this later in your workflow by selecting the Sample tags menu in the Experiment navigation bar.

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4. Review or adjust your panel assignments or channel names? For the last step, click on the Sample tags menu and select Assign panels to view and edit channel names.

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Once you are done setting up the new experiment, click on the step number 5 to start exploring your data, running advance analyses or creating reports.

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If you've already uploaded files to an experiment and want to upload more, you can do that by opening the Actions menu in the Experiment navigation bar, choosing Upload, and then Upload more files. While the set up wizard won’t reappear if you had already completed setup of the experiment, you can annotate the new files or adjust scaling and compensation as needed using the Experiment navigation bar menus.

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(upload more files to an experiment)

 

Remember, if you already have data on the Cytobank platform and want to use it in a different experiment, you can simply copy your experiment by cloning it.

You might also be interested in learning about uploading data via ACS, which allows the transfer of entire experiments between Cytobank servers. 

You can also create a new experiment and upload data using the KaluzaCytobank plugin. This approach takes advantage of the Kaluza Software analysis tools prior to running other machine learning algorithms on the Cytobank platform.

 

 
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