July 31, 2013  |  Education, Flow Cytometry

Cytometry for Interns

As a summer intern at Cytobank, the past few months have been busy and interesting to say the least. I am currently an undergraduate from the University of Redlands in Southern California. Although I have only been exposed to two years of introductory science courses, I have found that not only has it been easy to adjust to the research environment at the Nolan Lab at Stanford and the collegial atmosphere of Cytobank Inc, it has also been remarkably manageable to learn about flow cytometry.

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June 29, 2013  |  Education, Flow Cytometry

Garry Nolan Interview – Why is this single cell stuff so important?

Garry Nolan was recently interviewed by the science blog MendelsPod.com. Garry discusses the origins of his interest in single cell analysis, his lab’s work with Mass Cytometry, and moving past scientific low hanging fruit. He also discusses how his lab makes their techniques publicly available to the scientific community, and even gives his opinion on radical life extension. You can find the interview here, or you can read our summary below.

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October 30, 2011  |  Flow Cytometry

Cloning Experiments in Cytobank

Something we’ve found useful in analyzing our own data here at Cytobank is the ability to clone an experiment instead of having to download and re-upload files. If a colleague has shared an experiment with you and you don’t want to erase their hard work as you begin your analysis, make a clone! If you simply want to save time performing iterations of your own experiment analysis, make a clone! Experiment clones link back to the original experiments from which they were created on the Experiment Details page, so you’ll always have easy access to the original context. We’ve given you a variety of options for cloning, and you can find them under the “Cloning/Copying” section of the Actions box on the Experiment Details page.



Choosing to clone an experiment makes a full copy of the experiment, complete with all FCS files, gates, annotations, reagent labels, compensation matrices, protocols, and attachments. Let’s suppose a collaborator has shared an experiment with you. You want to tweak the existing gates without having to redraw them entirely, but don’t want to overwrite the collaborator’s own gates. You can clone a full copy of the experiment and then make the changes in your clone, saving yourself the time that would have been spent redrawing gates and the headache of realizing you erased someone else’s hard work. From an organizational standpoint, you may also want to clone a copy of an experiment shared with you if you want a copy that contains only your own saved illustrations, notes, and attachments, including presentations.

With your own experiments, you might also want to make full clones if you want to subtly tweak existing gates or annotations to perform slightly varying analyses of your own data. “Clone Experiment” can help you do just that.

When you clone an experiment, the clone name contains “(Clone)” at the end, by default.


Selective Cloning allows you to choose subsets of FCS files to copy into a new experiment while specifying whether to bring over the gates, compensation matrices, annotations, reagent labels, protocols, and attachments – you can choose to copy over some or all of these components, helping you make copies of experiments that can be analyzed in different ways. Perhaps you want to preserve how files are categorized into Conditions and Timepoints, but draw gates from scratch for an alternative analysis – use Selective Clone to clone all files with all annotation, but no gates. Maybe you want to alter how files are categorized into Conditions and Sample Types, but want to preserve gated populations – use Selective Clone to copy all files and gates, but none of the annotations. Selective Clone can help you perform iterations of experiment analysis without having to start from scratch, whether on your own experiments or experiments shared with you.

You can also use Selective Clone to split off smaller pieces of a large experiment for separate analysis, or to separate files that require different annotation, gating, or compensation.


There may be times when you want a completely fresh start, for example if you are using a dataset to teach flow cytometry analysis, or if you are a computational biologist trying to automate analysis. Clone FCS files is also useful if you want to share only the raw data with a colleague without sharing your analyses and other related information. By cloning FCS files only, you are copying the raw data into a new experiment without bringing over any gates, annotations, reagent labels, compensation matrices, protocols, and attachments that are associated with the original experiment.

Let us know if you have any questions about this functionality or any others!

– Angela

September 22, 2011  |  Flow Cytometry

Deconvolute, Decode, Decipher! How to Split, Tag, and Analyze Your Barcoded Data on Cytobank

You may have heard about Fluorescent Cell Barcoding, a flow cytometry technique that allows researchers to answer a larger number of questions with the same amount of antibody, as compared to standard flow cytometry experiments [1,2]. We’ve prepared a few resources to help you learn about, perform, and analyze barcoding experiments.


How does barcoding work? In the barcoding step, samples treated under different stimulation conditions are labeled with concentrations of dye that increase at a defined interval. The use of this dye to barcode effectively means that one cytometer channel is taken up for this code. The distinctly stimulated and labeled samples are then combined into one tube and stained with antibodies against targets of interest. This single tube is then run on a flow cytometer and data are collected for analysis. The most common approach is to barcode different stimulation conditions; however, barcoding can be applied to any distinct populations, such as patient samples or different time points of a stimulation condition.

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September 7, 2011  |  Flow Cytometry

Analyzing Hematopoietic Stem Cell Enrichment Data in Cytobank

Dataset #8414: Human Cord Blood – HSC isolation


Hematopoietic Stem Cells (HSCs) give rise to all blood lineages and are capable of self-renewal. Clinically, HSC transplantation is under investigation for the treatment of diseases of the blood and bone marrow, including cancer, where a patient’s blood cells are wiped out and replaced with healthy cells that arise from transplanted donor HSCs. Transplant studies in mice have shown that only a few of these cells are necessary to repopulate the entire hematopoietic system.

Human umbilical cord blood is a rich source of stem cells, including HSCs. However, a variety of other cell types populate cord blood and must be removed from HSC preparations used for transplantation. Multipotent progenitor cells (MPPs) are one such population. Derived from HSCs, MPPs give rise to multiple lineages and are present in significant quantities in cord blood, though they are limited in their capacity for self-renewal. Purification of HSCs can be achieved by staining and running cord blood through a FACS sorter and isolating cells with a Lin-CD34+CD38-CD90+CD45RA- surface signature (as defined by Park, Majeti, and Weissman). MPPs can be quantified or isolated by their Lin-CD34+CD38-CD90-CD45RA- signature.

Sample Data

If you would like to try your hand at analyzing HSC enrichment data on Cytobank, we have made available an HSC dataset provided to us by scientists at BD Biosciences. You can find a tutorial to guide your analysis on our documentation site. More »

August 23, 2011  |  Education, Flow Cytometry

Future Proofing Your Experiments and Files: The Importance of Annotation

Ever find yourself staring at a folder of FCS files and thinking, “Wait, now which tubes did I add PMA to, how much did I add, and which samples were these again?”

Jonathan from Cytobank/Stanford recommends what he calls “future proofing” in order to avoid this problem. He explained this approach during a CYTO 2011 Pre-Congress course in his talk titled “Flood Cytometry: Embracing Single Cell Systems Biology (and coping with large cytometry experiments).” In that talk, he outlined four easy steps that are useful for experiments of all sizes.

When collecting on the cytometer:

  1. Tag your FCS files with key experiment details (e.g. “Patient-J01 IL-2 15m”)
  2. Label the channels you are measuring (before collecting data)
  3. Make sure scales and compensations work (before collecting data)
  4. Encode clinical sample IDs (don’t use HIPAA sensitive information)
Click the image to download as a PPT slide

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July 21, 2011  |  Flow Cytometry

Naming and Exporting Files in Diva

Many of our users upload data to Cytobank that were collected on a BD Biosciences flow cytometer using BD FACSDiva™ software. In this post, we will walk you through how to harness the power of naming files in Diva to facilitate analysis on Cytobank and how to export FCS files from Diva for upload to Cytobank.

Detailed naming of sample files in Diva gives you a special advantage unique to Cytobank’s analysis environment. When you upload files to Cytobank, our servers will automatically categorize your files for ease of analysis when you annotate Figure Dimensions. This automated categorization enables you to rapidly generate well-annotated plot layouts and figures. Watch our YouTube video demonstrating this feature!

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June 17, 2011  |  Announcements, Flow Cytometry

BD FACSelect™: Resources to Optimize Your Flow Experiments

Designing a successful flow experiment – selecting compatible reagents and optimizing your protocol – can be challenging and time-consuming. And yet, as we all know, a well-designed experiment is critical to the collection of high-quality flow data.

What do we think about when designing flow experiments?

  • What buffers should I use when probing intracellular targets?
  • Which surface antibodies work well on my sample and with my buffers?
  • What is the best concentration for my antibody?
  • Are there alternative protocols that work better with my samples?

We are excited to announce the arrival of two resources that will help you answer those questions and streamline your reagent selection process. BD Biosciences has released the FACSelect™ series, consisting of a Multicolor Panel Designer and a Buffer Compatibility Resource.

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