September 29, 2016  |  Announcements, Cytobank, User Stories

Customer Story: Reema Baskar, Stanford Medicine

Welcome to Cytobank User Stories, a series featuring interviews with Cytobank users on their research, scientific vision, and use of fluorescence and mass cytometry.

This week we interview Reema Baskar, a graduate student in the Cancer Biology Department at Stanford University, co-mentored by Sean Bendall and Sylvia Plevritis. We asked Reema about how she uses Cytobank’s high-dimensional tools to help elucidate mechanisms of drug resistance in cancer, and her early experience beta-testing our new CITRUS implementation.

What is an important problem in human health and/or fundamental biology that you’d like to address? What is your scientific vision?
Reema Baskar
Cancer Biology Dept.
Stanford University

My vision is to develop high-dimensional techniques and computational tools to address the challenge of ‘big data.’ My hope is that these tools may be broadly applied to aid our understanding of the human condition. Technology, such as mass cytometry (CyTOF), has made it possible to capture different facets of biology such as cell function, epigenetic traits, and transcriptional readouts with infinitesimal single-cell granularity. More »

August 31, 2016  |  Announcements, API, Cytobank, Release Notes

Streamline and Automate Analysis with Our New API

CytobankAPIAchieve better results, faster. Automate your end-to-end pipelines with the Cytobank Platform via The Cytobank APIThe Cytobank API extends the power of the Cytobank Cloud to any software application. Now bench scientists can more seamlessly interact with computational biologists and reviewers to assess results of internal algorithms and pipelines. 

Now available in the Enterprise versionour RESTful API endpoints offer powerful advantages More »

August 12, 2015  |  Announcements, Publications

A Framework for Modeling the Immune System

Spitzer and Gherardini et al., from the Nolan Lab at Stanford University, report a novel bioinformatics approach to mapping the immune system called Scaffold (Single-Cell Analysis by Fixed Force- and Landmark-Directed).

Scaffold allows clustering of samples independently, thus allowing addition of new sample data over time. This approach requires users to develop or use a pre-defined reference map.

In their recent publication in Science, the authors reveal maps comparing immune organization among several tissue compartments, among mouse strains, between circadian states, and between species (mouse and human).
More »

June 19, 2015  |  Announcements, Cytobank, Flow Cytometry

Visit us at CYTO and FOCiS!

Come visit the Cytobank team at FOCiS and CYTO next week to learn more about what we’ve been up to, for some hands-on help, to share your wish list or just to chit-chat. We look forward to seeing you there!

Check out the various talks and posters at CYTO featuring Cytobank:

Saturday June 27, 2015

11:00 (Room: Alsh) – The First Multi-center Comparative Study Using a Novel Technology Mass Cytometry Time-of-Flight Mass Spectrometer (CyTOF2) for High-Speed Acquisition of Highly Multi-parametric Single Cell Data: A Status Report A. Nasaar, B. Carter, J. Lannigan, R. Montgomery, N. Paul, M. Poulin, K. Raddassi, A. Rahman and N. Rashidi. Yale Univ. Sch. of Med., Stanford Shared FACS Facilities, Univ. of Virginia Sch. of Med., Dana-Farber Cancer Inst., Fluidigm, Cambridge, MA, Icahn Sch. of Med. at Mount Sinai and Ragon Inst. of MGH, MIT and Harvard.

11:40 (Room: Alsh) – High Content Dissection of Human Melanoma Tumor Heterogeneity during Treatment Using Mass Cytometry J. Irish, D. Doxie, A. Greenplate, K. Diggins, H. Polikowsky, K. Dahlman, J. Sosman and M. Kelley. Vanderbilt Univ. Sch. of Med.

More »

March 12, 2015  |  Announcements, Education

Complete your viSNE workflow and back-gate using Dot Overlays

Always listening to our user feedback, we heard your requests to complete your viSNE workflow by overlaying Populations to uniquely color the viSNE continents. Our latest release brings you a new plot type configuration we call Dot Overlays that allows you to do this, and also lends itself to traditional back-gating approaches that allow you to see child populations in the context of ancestors.

Dot Overlays
Dot Overlays

Dot Overlays allow you to overlay not just Populations, but any of the Figure Dimensions within a single Dot Plot. Now you can compare Populations, Timepoints, Conditions, Individuals, and any dimension of your choosing within Dot Overlay plots. Just drag any figure dimension into the second (overlaid) position. See how your time course stacks out, compare your stimulations/titration data, or just see how populations sit in the context of each other (traditional back-gating). Visit our knowledge base for the full scoop on how to set up Dot Overlays, including a video tutorial.
More »

February 5, 2015  |  Announcements, Publications, User Stories

New Breakthrough Method in Mass Cytometry

Zunder and Finck et al., from the Nolan Lab at Stanford University report new cell barcoding reagents for mass cytometry that incorporate the previously unused element palladium, expanding the number of mass cytometry measurement parameters by six. Leveraging this methodology, they present a new barcoding scheme which can be used to identify and remove cell doublets, as well as provide software that deconvolves barcoded datasets via a “single-cell debarcode” algorithm [1].

The dataset for this paper is hosted and publicly available on Cytobank Community; a free resource for the analysis, workflow, and protocols represented in this paper. Cytobank is the cloud-based analytics platform for single cell analysis. In Cytobank you can easily access and analyze multi-parameter data, visualize findings, produce high-impact graphics, and securely connect and collaborate with colleagues around the world.

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November 13, 2014  |  Announcements, Cytobank

viSNE now available on Cytobank

The Cytobank team has been working diligently to provide top tier analysis solutions for our users; viSNE in Cytobank is our most recent addition and we are very excited about what it has to offer.

What is viSNE? And how does it work?

viSNE is a tool for reducing high-parameter data down to two dimensions, making it easy for scientists to not only visually identify interesting and rare biological subsets, but also gate single cell events across different samples.

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November 10, 2014  |  Announcements, User Stories

Behbehani et al. Transient Partial Permeabilization with Saponin Enables Cellular Barcoding Prior to Surface Marker Staining.

Greg BehbehaniGreg Behbehani, a physician scientist, is focused on translational research, leveraging his work treating patients in clinical trials for high-risk hematologic malignancies towards the ultimate goal of utilizing data generated in the laboratory to predict ideal chemotherapy regimens and optimal novel agents for individual patients.

Most recently Dr. Behbehani has contributed to a published paper surrounding research of new protocols for barcoding on mass and fluorescence cytometry [1]. The dataset is hosted and publicly available on Community Cytobank; a free resource for individuals interested in the analysis, workflow, and protocols represented in this paper.

More »