scholarly journals High-Speed Automatic Characterization of Rare Events in Flow Cytometric Data

2019 ◽  
Author(s):  
Yuan Qi ◽  
Youhan Fang ◽  
David R. Sinclair ◽  
Shangqin Guo ◽  
Meritxell Alberich-Jorda ◽  
...  

AbstractA new computational framework for FLow cytometric Analysis of Rare Events (FLARE) has been developed specifically for fast and automatic identification of rare cell populations in very large samples generated by platforms like multi-parametric flow cytometry. Using a hierarchical Bayesian model and information-sharing via parallel computation, FLARE rapidly explores the high-dimensional marker-space to detect highly rare populations that are consistent across multiple samples. Further it can focus within specified regions of interest in marker-space to detect subpopulations with desired precision.

PLoS ONE ◽  
2020 ◽  
Vol 15 (2) ◽  
pp. e0228651
Author(s):  
Yuan Qi ◽  
Youhan Fang ◽  
David R. Sinclair ◽  
Shangqin Guo ◽  
Meritxell Alberich-Jorda ◽  
...  

1992 ◽  
Vol 166 (1) ◽  
pp. 65-73 ◽  
Author(s):  
M. R. Yeaman ◽  
P. M. Sullam ◽  
P. F. Dazin ◽  
D. C. Norman ◽  
A. S. Bayer

2019 ◽  
Vol 317 (3) ◽  
pp. H658-H666 ◽  
Author(s):  
Roman Covarrubias ◽  
Mohamed Ameen Ismahil ◽  
Gregg Rokosh ◽  
Tariq Hamid ◽  
Federica Accornero ◽  
...  

Immune activation post-myocardial infarction is an orchestrated sequence of cellular responses to effect tissue repair and healing. However, excessive and dysregulated inflammation can result in left ventricular remodeling and pathological alterations in the structural and mechanical attributes of the heart. Identification of key pathways and critical cellular mediators of inflammation is thus essential to design immunomodulatory therapies for myocardial infarction and ischemic heart failure. Despite this, the experimental approaches to isolate mononuclear cells from the heart are diverse, and detailed protocols to enable maximum yield of live cells in the shortest time possible are not readily available. Here, we describe optimized protocols for the isolation, fixation, and flow cytometric characterization of cardiac CD45+ leukocytes. These protocols circumvent time-consuming coronary perfusion and density-mediated cell-separation steps, resulting in high cellular yields from cardiac digests devoid of contaminating intravascular cells. Moreover, in contrast to methanol and acetone, we show that cell fixation using 1% paraformaldehyde is most optimal as it does not affect antibody binding or cellular morphology, thereby providing a considerable advantage to study activation/infiltration-associated changes in cellular granularity and size. These are highly versatile methods that can easily be streamlined for studies requiring simultaneous isolation of immune cells from different tissues or deployment in studies containing a large cohort of samples with time-sensitive constraints. NEW & NOTEWORTHY In this article, we describe optimized protocols for the isolation, fixation, and flow cytometric analysis of immune cells from the ischemic/nonischemic hearts. These protocols are optimized to process several samples/tissues, simultaneously enabling maximal yield of immune cells in the shortest time possible. We show that the low-speed centrifugation can be used as an effective alternative to lengthy coronary perfusion to remove intravascular cells, and sieving through 40-μm filter can replace density-mediated mononuclear cell separation which usually results in 50–70% cell loss in the sedimented pellets. We also show that cell fixation using 1% paraformaldehyde is better than the organic solvents such as methanol and acetone for flow cytometric analysis.


2014 ◽  
Vol 413 ◽  
pp. 45-56 ◽  
Author(s):  
Maren Kuhne ◽  
Martin Dippong ◽  
Sabine Flemig ◽  
Katrin Hoffmann ◽  
Kristin Petsch ◽  
...  

2000 ◽  
Vol 182 (11) ◽  
pp. 3289-3291 ◽  
Author(s):  
Lyudmila I. Rachek ◽  
Andria Hines ◽  
Aimee M. Tucker ◽  
Herbert H. Winkler ◽  
David O. Wood

ABSTRACT Rickettsia prowazekii, the etiologic agent of epidemic typhus, is an obligate, intracytoplasmic, parasitic bacterium. Recently, the transformation of this bacterium via electroporation has been reported. However, in these studies identification of transformants was dependent upon either selection of an R. prowazekii rpoB chromosomal mutation imparting rifampin resistance or expression of the green fluorescent protein and flow cytometric analysis. In this paper we describe the expression inR. prowazekii of the Escherichia coli ereBgene. This gene codes for an erythromycin esterase that cleaves erythromycin. To the best of our knowledge, this is the first report of the expression of a nonrickettsial, antibiotic-selectable gene inR. prowazekii. The availability of a positive selection for rickettsial transformants is an important step in the characterization of genetic analysis systems in the rickettsiae.


1992 ◽  
Vol 8 (1) ◽  
pp. 65-74 ◽  
Author(s):  
José M. Coco-Martin ◽  
Jan W. Oberink ◽  
Tiny A. M. van der Velden-de Groot ◽  
E. Coen Beuvery

Cytometry ◽  
1994 ◽  
Vol 15 (3) ◽  
pp. 230-236 ◽  
Author(s):  
Ger J. J. C. Boonen ◽  
Ben M. de Koster ◽  
Maarten van der Keur ◽  
John Vansteveninck ◽  
Hans J. Tanke ◽  
...  

1993 ◽  
Vol 3 (2) ◽  
pp. 103-112 ◽  
Author(s):  
Mireille Lahoud ◽  
David Vremec ◽  
Richard L. Boyd ◽  
Ken Shortman

Thymic nurse cells (TNC), multicellular complexes consisting of lymphoid cells enclosed within cortical epithelial cells, were isolated from mouse thymus by a modified procedure allowing immunofluorescent labeling and flow cytometric analysis of their lymphoid contents (TNC-L). Collagenase was the only protease used for tissue digestion, to ensure that surface antigen markers remained intact. Zonal unit-gravity elutriation was used to enrich the TNC on the basis of their high sedimentation rate, followed by immunomagnetic bead depletion to remove residual mononuclear cell contaminants and a density separation to remove debris. The TNC-L were then released from inside TNC by a short period of culture. The measured contamination of TNC-L with exogenous thymocytes was around 0.5%. Three-color immunofluorescent labeling revealed that TNC-L included, as well as a maiority of immature CD4+8+3lowthymocytes, about 12% of apparently mature CD4+8-3highand CD4-8+3highthymocytes. TNC are located in the cortex, where mature cells are rare; the occurrence of mature phenotype cells within these structures suggests that they represent a microenvironment for the selection and generation of mature T cells.


Blood ◽  
2012 ◽  
Vol 120 (21) ◽  
pp. 4839-4839
Author(s):  
Anne Richter ◽  
Michaela Niemöller ◽  
Inken Verwohl ◽  
Katrin Lange ◽  
Anna Foerster-Marniok ◽  
...  

Abstract Abstract 4839 Functional characterizations of T lymphocytes are performed to gain understanding on their contribution in certain immunological situations, to monitor the course of diseases, and to track therapeutic interventions. Meanwhile the flow cytometric analysis of antigen-specific T cells examined for intracellular cytokine production and expression of activation markers after a short-term in vitro antigenic challenge is a well-established method for research applications. Despite the advantages of this approach to qualify samples on a single cell level and by multiple parameters, the broad use of this analysis for immune monitoring purposes is hampered. Screening of a lot of samples is time-consuming, requires many manual handling steps, and operator experience in flow cytometric analysis of stimulated T cell samples. To overcome these hurdles, we worked out a complete strategy to rapidly study cytokine and activation marker profiles in antigen-specific T cells of multiple samples by a semi-automated process. For the simultaneous analysis of multiple samples we examined for the T cell stimulation an antigen pre-coated 96-strip-well culture system. This flexible and ready-to-use format provides the opportunity to screen either for a single antigen or in parallel for up to twelve antigen specificities by combining 8-well-strips possessing different antigens. The coated antigens consist of pools of overlapping 15-mer peptides derived from a single viral protein of cytomegalovirus, Epstein-Barr-Virus, or adenovirus. The peptide pools have been designed for activation of the specific CD4+ as well as CD8+ T cells. They are solubilized and thereby accessible for T cell stimulation after addition of a cell sample, e.g. peripheral blood mononuclear cells, suspended in culture medium into the antigen-coated well. After a stimulation period of six hours the induced T cell response is comparable to the activation with a conventional lyophilized and reconstituted peptide pool. To reduce the time and work load for cell harvesting, fixation, permeabilization, and staining, we developed a protocol and reagents to allow a rapid and easy-to-handle intracellular staining procedure. Compared to conventional staining protocols, all steps are executed in the 96-strip-well culture plate, i.e. cell harvesting is dispensable. Without any washing step, cells are fixed and stained with defined reagent cocktails containing antibodies to identify virus-specific CD3+ CD4+ CD154+ and/or CD3+ CD8+ T cells and various Anti-cytokine-fluorochrome conjugates to evaluate the cytokine pattern. With these modifications, we drastically diminished the overall processing time for the staining of up to 96 samples to only 50 minutes. Furthermore, we integrated an automated flow cytometric analysis process. This includes the possibility to measure the samples in the 96-strip-well plates hands-free using pre-defined experiment settings and acquisition templates. We also applied an automated gating strategy for the data analysis. Finally, a report summarizes the results of the T cell response against several viral proteins for all samples tested, e.g. frequencies of cytokine+ CD154+ CD4+ and cytokine+ CD8+ T cell subsets are indicated. Hands-on time for the multi-sample acquisition and analysis is only minimal and the standardized reagents/protocol and sample analysis process decrease inter- and intra-assay variations. In summary, with our newly developed tools and protocols for in vitro T cell stimulation, staining of activation markers as well as intracellular cytokines, and automated flow cytometric analysis we have set up a fast and convenient procedure to routinely monitor antigen-specific T cell responses. Disclosures: Richter: Miltenyi Biotec GmbH: Employment. Niemöller:Miltenyi Biotec GmbH: Employment. Verwohl:Miltenyi Biotec GmbH: Employment. Lange:Miltenyi Biotec GmbH: Employment. Foerster-Marniok:Miltenyi Biotec GmbH: Employment. Brauns:Miltenyi Biotec GmbH: Employment. Kramer:Miltenyi Biotec GmbH: Employment. Höher-Peters:Miltenyi Biotec GmbH: Employment. Büscher:Miltenyi Biotec GmbH: Employment. Assenmacher:Miltenyi Biotec GmbH: Employment. Schmitz:Miltenyi Biotec GmbH: Employment.


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