Literature DB >> 20578106

Web-based analysis and publication of flow cytometry experiments.

Nikesh Kotecha1, Peter O Krutzik, Jonathan M Irish.   

Abstract

Cytobank is a Web-based application for storage, analysis, and sharing of flow cytometry experiments. Researchers use a Web browser to log in and use a wide range of tools developed for basic and advanced flow cytometry. In addition to providing access to standard cytometry tools from any computer, Cytobank creates a platform and community for developing new analysis and publication tools. Figure layouts created on Cytobank are designed to allow transparent access to the underlying experiment annotation and data processing steps. Since all flow cytometry files and analysis data are stored on a central server, experiments and figures can be viewed or edited by anyone with the proper permission, from any computer with Internet access. Once a primary researcher has performed the initial analysis of the data, collaborators can engage in experiment analysis and make their own figure layouts using the gated, compensated experiment files. Cytobank is available to the scientific community at http://www.cytobank.org. (c) 2010 by John Wiley & Sons, Inc.

Entities:  

Mesh:

Year:  2010        PMID: 20578106      PMCID: PMC4208272          DOI: 10.1002/0471142956.cy1017s53

Source DB:  PubMed          Journal:  Curr Protoc Cytom        ISSN: 1934-9297


  9 in total

1.  Intracellular phospho-protein staining techniques for flow cytometry: monitoring single cell signaling events.

Authors:  Peter O Krutzik; Garry P Nolan
Journal:  Cytometry A       Date:  2003-10       Impact factor: 4.355

2.  Causal protein-signaling networks derived from multiparameter single-cell data.

Authors:  Karen Sachs; Omar Perez; Dana Pe'er; Douglas A Lauffenburger; Garry P Nolan
Journal:  Science       Date:  2005-04-22       Impact factor: 47.728

3.  Fluorescent cell barcoding in flow cytometry allows high-throughput drug screening and signaling profiling.

Authors:  Peter O Krutzik; Garry P Nolan
Journal:  Nat Methods       Date:  2006-05       Impact factor: 28.547

4.  NCBI GEO: archive for high-throughput functional genomic data.

Authors:  Tanya Barrett; Dennis B Troup; Stephen E Wilhite; Pierre Ledoux; Dmitry Rudnev; Carlos Evangelista; Irene F Kim; Alexandra Soboleva; Maxim Tomashevsky; Kimberly A Marshall; Katherine H Phillippy; Patti M Sherman; Rolf N Muertter; Ron Edgar
Journal:  Nucleic Acids Res       Date:  2008-10-21       Impact factor: 16.971

5.  Single cell profiling of potentiated phospho-protein networks in cancer cells.

Authors:  Jonathan M Irish; Randi Hovland; Peter O Krutzik; Omar D Perez; Øystein Bruserud; Bjørn T Gjertsen; Garry P Nolan
Journal:  Cell       Date:  2004-07-23       Impact factor: 41.582

Review 6.  Mapping normal and cancer cell signalling networks: towards single-cell proteomics.

Authors:  Jonathan M Irish; Nikesh Kotecha; Garry P Nolan
Journal:  Nat Rev Cancer       Date:  2006-02       Impact factor: 60.716

7.  The Stanford Microarray Database: implementation of new analysis tools and open source release of software.

Authors:  Janos Demeter; Catherine Beauheim; Jeremy Gollub; Tina Hernandez-Boussard; Heng Jin; Donald Maier; John C Matese; Michael Nitzberg; Farrell Wymore; Zachariah K Zachariah; Patrick O Brown; Gavin Sherlock; Catherine A Ball
Journal:  Nucleic Acids Res       Date:  2006-12-20       Impact factor: 16.971

8.  flowCore: a Bioconductor package for high throughput flow cytometry.

Authors:  Florian Hahne; Nolwenn LeMeur; Ryan R Brinkman; Byron Ellis; Perry Haaland; Deepayan Sarkar; Josef Spidlen; Errol Strain; Robert Gentleman
Journal:  BMC Bioinformatics       Date:  2009-04-09       Impact factor: 3.169

9.  Flow: Statistics, visualization and informatics for flow cytometry.

Authors:  Jacob Frelinger; Thomas B Kepler; Cliburn Chan
Journal:  Source Code Biol Med       Date:  2008-06-17
  9 in total
  206 in total

1.  CytoSPADE: high-performance analysis and visualization of high-dimensional cytometry data.

Authors:  Michael D Linderman; Zach Bjornson; Erin F Simonds; Peng Qiu; Robert V Bruggner; Ketaki Sheode; Teresa H Meng; Sylvia K Plevritis; Garry P Nolan
Journal:  Bioinformatics       Date:  2012-07-10       Impact factor: 6.937

2.  Isolation of adipose tissue immune cells.

Authors:  Jeb S Orr; Arion J Kennedy; Alyssa H Hasty
Journal:  J Vis Exp       Date:  2013-05-22       Impact factor: 1.355

3.  Mitochondrial dysregulation and glycolytic insufficiency functionally impair CD8 T cells infiltrating human renal cell carcinoma.

Authors:  Peter J Siska; Kathryn E Beckermann; Frank M Mason; Gabriela Andrejeva; Allison R Greenplate; Adam B Sendor; Yun-Chen J Chiang; Armando L Corona; Lelisa F Gemta; Benjamin G Vincent; Richard C Wang; Bumki Kim; Jiyong Hong; Chiu-Lan Chen; Timothy N Bullock; Jonathan M Irish; W Kimryn Rathmell; Jeffrey C Rathmell
Journal:  JCI Insight       Date:  2017-06-15

4.  Genetic Inactivation of CD33 in Hematopoietic Stem Cells to Enable CAR T Cell Immunotherapy for Acute Myeloid Leukemia.

Authors:  Miriam Y Kim; Kyung-Rok Yu; Saad S Kenderian; Marco Ruella; Shirley Chen; Tae-Hoon Shin; Aisha A Aljanahi; Daniel Schreeder; Michael Klichinsky; Olga Shestova; Miroslaw S Kozlowski; Katherine D Cummins; Xinhe Shan; Maksim Shestov; Adam Bagg; Jennifer J D Morrissette; Palak Sekhri; Cicera R Lazzarotto; Katherine R Calvo; Douglas B Kuhns; Robert E Donahue; Gregory K Behbehani; Shengdar Q Tsai; Cynthia E Dunbar; Saar Gill
Journal:  Cell       Date:  2018-05-31       Impact factor: 41.582

5.  Human Fallopian Tube Epithelial Cell Culture Model To Study Host Responses to Chlamydia trachomatis Infection.

Authors:  Scott H Randell; Toni Darville; Uma M Nagarajan; Bryan E McQueen; Amy Kiatthanapaiboon; M Leslie Fulcher; Mariam Lam; Kate Patton; Emily Powell; Avinash Kollipara; Victoria Madden; Robert J Suchland; Priscilla Wyrick; Catherine M O'Connell; Boris Reidel; Mehmet Kesimer
Journal:  Infect Immun       Date:  2020-08-19       Impact factor: 3.441

6.  Single-cell trajectory detection uncovers progression and regulatory coordination in human B cell development.

Authors:  Sean C Bendall; Kara L Davis; El-Ad David Amir; Michelle D Tadmor; Erin F Simonds; Tiffany J Chen; Daniel K Shenfeld; Garry P Nolan; Dana Pe'er
Journal:  Cell       Date:  2014-04-24       Impact factor: 41.582

7.  Tumor-specific MHC-II expression drives a unique pattern of resistance to immunotherapy via LAG-3/FCRL6 engagement.

Authors:  Douglas B Johnson; Mellissa J Nixon; Yu Wang; Daniel Y Wang; Emily Castellanos; Monica V Estrada; Paula I Ericsson-Gonzalez; Candace H Cote; Roberto Salgado; Violeta Sanchez; Phillip T Dean; Susan R Opalenik; Daniel M Schreeder; David L Rimm; Ju Young Kim; Jennifer Bordeaux; Sherene Loi; Leora Horn; Melinda E Sanders; P Brent Ferrell; Yaomin Xu; Jeffrey A Sosman; Randall S Davis; Justin M Balko
Journal:  JCI Insight       Date:  2018-12-20

8.  High-dimensional single cell mapping of cerium distribution in the lung immune microenvironment of an active smoker.

Authors:  Adeeb H Rahman; Yonit Lavin; Soma Kobayashi; Andrew Leader; Miriam Merad
Journal:  Cytometry B Clin Cytom       Date:  2017-08-07       Impact factor: 3.058

9.  High-Dimensional Data Analysis Algorithms Yield Comparable Results for Mass Cytometry and Spectral Flow Cytometry Data.

Authors:  Laura Ferrer-Font; Johannes U Mayer; Samuel Old; Ian F Hermans; Jonathan Irish; Kylie M Price
Journal:  Cytometry A       Date:  2020-04-15       Impact factor: 4.355

10.  MICA variant promotes allosensitization after kidney transplantation.

Authors:  Pierre Tonnerre; Nathalie Gérard; Mathias Chatelais; Caroline Poli; Stéphanie Allard; Sylvie Cury; Céline Bressollette; Anne Cesbron-Gautier; Béatrice Charreau
Journal:  J Am Soc Nephrol       Date:  2013-03-28       Impact factor: 10.121

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