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Overview of uploading data to Cytobank

Create an experiment to upload the data

Before uploading data, you must register a Cytobank account on the 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 next to the Cytobank logo on the top.

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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, perform data QC, annotate Sample tags and review. It will walk through the steps to set up your data for further analysis and reporting.  

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Tips: Once you finish setting up the previous step, go back to the Set up new experiment page by clicking on the in-app back arrowor the browser back arrow

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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 the tab to open up the scales window to adjust the scaling. Click on Learn more if you need more information about the scales on 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. 

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  1. Set the experiment compensation

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

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  1. Perform DataQC

Run the PeacoQCprocess to perform DataQC and remove low-quality events from your FCS files. You may click on Learn more to get more information on the PeacoQC data QC

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4. 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 Conditions, Doses, Individuals, Reagents, Timepoints, or a custom dimension. 

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5. Review or adjust your panel assignments or channel names

The next 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 text: Done with setup and ready to start exploring your experiment data?to reveal the Analysis and Reporting menu options. You can start to run advanced analyses or create reports.

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Add more files to an existing experiment

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 new experiment landing page won’t reappear if you had already completed setup of the experiment, you could 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)

Have more questions? Submit a request

 



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