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opencc-by-4.0Dec 2017View details →

Fig. 3 in Bottlenose dolphins (Tursiops truncatus) do also cast neutrophil extracellular traps against the apicomplexan parasite Neospora caninum

Fig. 3. Dose, kinetic and functional inhibition assays of N. caninum tachyzoites-triggered NET formation in dolphins. PMN were incubated with tachyzoites, zymosan (1 mg/ ml, positive control) or plain medium (negative control) at different ratios (a; PMN: tachyzoites = 1:1, 1:2, 1:3) and time periods (b; 30, 60 and 90 min). To prove the DNA nature of NETs, the samples were treated with DNase I (a; 15 min). Moreover, cetacean PMN cells were pre-treated with NOX-inhibitor (b; DPI, 10 MM) for 30 min prior to N. caninum stimulation (1:3 ratio; 90 min). After incubation, all samples were analyzed for extracellular DNA by quantifying Pico Green ®-derived fluorescence intensities. Each condition was performed in duplicates. Geometric means of three PMN donors. Differences were regarded as significant at a level of p <0.05 (*) and p <0.01 (**).

opencc-by-4.0Dec 2017View details →

Fig. 2 in Bottlenose dolphins (Tursiops truncatus) do also cast neutrophil extracellular traps against the apicomplexan parasite Neospora caninum

Fig. 2. Neospora caninum tachyzoite-triggered dolphin NET structures (SEM) and co-localization of extracellular DNA with histones (H1, H2A/H2B, H3 and H4), NE, MPO and PTX. (a‾d) Scanning electron microscopy (SEM) analyses revealed NETs being formed by dolphin PMN after co-culture with N. caninum tachyzoites. (a) Mesh of DNA-structures (white arrow) derived from dolphin PMN attached to N. caninum-tachyzoites (black arrows). (b) Intact cetacean-PMN (black stars) derived a fine filaroid structure (white arrow) being attached to tachyzoites (black arrows). (c) Conglomerates of several tachyzoites (black arrow) being entrapped in a rather chunky meshwork of cetacean-PMN-released thicker extracellular filaments (white arrow) (d) Dolphin PMN activated (black star) entrapping diverse N. caninum-tachyzoites (black arrows). (e‾l) Co-cultures of dolphin PMN and N. caninum tachyzoites were fixed, permeabilized, stained for analysis of co-localization (i-l; merge, white arrows) of extracellular DNA (e-h; red; Sytox Orange ®) and classical NETs components (all green, white arrows) such as histones (i), NE (j), MPO (k) and pentraxin (l). (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)

opencc-by-4.0Dec 2017View details →

Fig. 1 in Bottlenose dolphins (Tursiops truncatus) do also cast neutrophil extracellular traps against the apicomplexan parasite Neospora caninum

Fig. 1. Minimally-invasive blood extraction method for cetaceans. (a) Puncture of the ventral superficial fluke plexus with a fine needle attached to infusion system and one syringe to create a vacuum for blood extraction. (b) Professional trainers performed physical restraint of one dolphin using whistle to give a positive reinforcement during sampling.

opencc-by-4.0Apr 2013View details →

Synthetic Data for Neutrophil Analysis: Sets with irregular shapes and Poisson noise

Synthetic Datasets with irregular shapes and Poisson noise. Part of the PhagoSight neutrophil tracking and analysis package (Henry, et al., PLOS ONE, 2013):   https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0072636 http://www.phagosight.org https://github.com/phagosight/phagosight   A series of synthetic data sets that reproduce different behaviour characteristics of migrating neutrophils were generated in MATLAB. The data sets consisted of six artificial neutrophils that travelled along paths that presented different conditions of tortuosity, times to activation and proximity to other neutrophils during 98 time frames. Numerous data sets of neutrophils in zebrafish were carefully observed before setting the characteristics. Six trajectories were manually determined by setting the row, column positions of the centroids at every time point for 98 time frames. Each trajectory was designed so that it would represent different neutrophil behaviours: some trajectories were very oriented and had movements with uniform distance between time frames, whilst others were less uniform and would move at different velocities, some were tortuous whilst others were straight. The trajectories of cells 1 and 2 collided several times in the second half of the time frames whilst cells 3 and 4 collided at the beginning of the movement. Cell 6 migrated without meandering and then stopped at the end (which represents the wound area of an inflammation-based experiment) whilst 5 presented a delayed activation.  Each time frame consisted of 11 slices of z-stack each with 275 x 275 pixels, where the neutrophils were formed by irregular shapes (sum of Gaussians) and Poisson Noise (check the corresponding sets with regular shapes, i.e. Gaussians with Gaussian noise plus another set with a single large neutrophil and Poisson noise) distributions of higher intensities than the background. The orientation of the Poisson varied according to the displacement of the artificial neutrophils, i.e.they were round when the cells were static, or elongated when in movement. The tracks with the Shapes were saved as the gold standard and five different data sets were generated by adding varying levels of white Poisson noise resulting in data sets with distributions with increasing similarity between the neutrophils and the background reflected by the decreasing values of the Bhattacharyya Distance (1.61, 1.25, 1, 0.66, 0.45) as defined by Coleman 1979.   Files corresponding to the sets with irregular shapes and Poisson noise (noise increases from 1 to 5): <ul> <li>    x,y,t trajectories    ThreeDTracks</li> <li>    Ground Truth       syntheticData_P_mat_La </li> <li>    First data set         syntheticData_P1_mat_Re</li> <li>    Second data set     syntheticData_P2_mat_Re</li> <li>    Third data set       syntheticData_P3_mat_Re</li> <li>    Fourth data set     syntheticData_P4_mat_Re</li> <li>    Fifth data set        syntheticData_P5_mat_Re</li> </ul> Corresponding GIF files are also included as illustrations of the cells in motion.   Main Reference: <a href="https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0072636">PhagoSight: An Open-Source MATLAB® Package for the Analysis of Fluorescent Neutrophil and Macrophage Migration in a Zebrafish Model </a> Henry KM, Pase L, Ramos-Lopez CF, Lieschke GJ, Renshaw SA, Reyes-Aldasoro CC. (2013) PhagoSight: An Open-Source MATLAB® Package for the Analysis of Fluorescent Neutrophil and Macrophage Migration in a Zebrafish Model. PLOS ONE 8(8): e72636. <a href="https://doi.org/10.1371/journal.pone.0072636">https://doi.org/10.1371/journal.pone.0072636</a>

opencc-by-4.0Apr 2013View details →

Synthetic Data for Neutrophil Analysis: Sets with regular shapes and Gaussian noise

Synthetic Datasets with regular shapes and Gaussian noise. Part of the PhagoSight neutrophil tracking and analysis package (Henry, et al., PLOS ONE, 2013):   https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0072636 http://www.phagosight.org https://github.com/phagosight/phagosight   A series of synthetic data sets that reproduce different behaviour characteristics of migrating neutrophils were generated in MATLAB. The data sets consisted of six artificial neutrophils that travelled along paths that presented different conditions of tortuosity, times to activation and proximity to other neutrophils during 98 time frames. Numerous data sets of neutrophils in zebrafish were carefully observed before setting the characteristics. Six trajectories were manually determined by setting the row, column positions of the centroids at every time point for 98 time frames. Each trajectory was designed so that it would represent different neutrophil behaviours: some trajectories were very oriented and had movements with uniform distance between time frames, whilst others were less uniform and would move at different velocities, some were tortuous whilst others were straight. The trajectories of cells 1 and 2 collided several times in the second half of the time frames whilst cells 3 and 4 collided at the beginning of the movement. Cell 6 migrated without meandering and then stopped at the end (which represents the wound area of an inflammation-based experiment) whilst 5 presented a delayed activation.  Each time frame consisted of 11 slices of z-stack each with 275 x 275 pixels, where the neutrophils were formed by Gaussian distributions of higher intensities than the background and Gaussian noise (check the corresponding irregular shapes with Poisson noise plus another set with a single large neutrophil and Poisson noise). The orientation of the Gaussians varied according to the displacement of the artificial neutrophils, i.e.they were round when the cells were static, or elongated when in movement. The tracks with the Gaussians were saved as the gold standard and five different data sets were generated by adding varying levels of white Gaussian noise resulting in data sets with distributions with increasing similarity between the neutrophils and the background reflected by the decreasing values of the Bhattacharyya Distance (1.61, 1.25, 1, 0.66, 0.45) as defined by Coleman 1979.   Files corresponding to the sets with irregular shapes and Poisson noise (noise increases from 1 to 6): <ul> <li>    x,y,t trajectories    ThreeDTracks</li> <li>    Ground Truth       syntheticData0_mat_Re </li> <li>    First data set         syntheticData1_mat_Re</li> <li>    Second data set     syntheticData2_mat_Re</li> <li>    Third data set       syntheticData3_mat_Re</li> <li>    Fourth data set     syntheticData4_mat_Re</li> <li>    Fifth data set         syntheticData5_mat_Re</li> <li>    Sixth data set         syntheticData6_mat_Re</li> </ul>   Corresponding GIF files are also included as illustrations of the cells in motion.   Main Reference: <a href="https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0072636">PhagoSight: An Open-Source MATLAB® Package for the Analysis of Fluorescent Neutrophil and Macrophage Migration in a Zebrafish Model </a> Henry KM, Pase L, Ramos-Lopez CF, Lieschke GJ, Renshaw SA, Reyes-Aldasoro CC. (2013) PhagoSight: An Open-Source MATLAB® Package for the Analysis of Fluorescent Neutrophil and Macrophage Migration in a Zebrafish Model. PLOS ONE 8(8): e72636. <a href="https://doi.org/10.1371/journal.pone.0072636">https://doi.org/10.1371/journal.pone.0072636</a>

opencc-by-4.0Sep 2021View details →

TIRF imaging data of neutrophils migrating underneath endothelial cells

This data is used in the publication "Endothelial Focal Adhesions Are Functional Obstacles for Leukocytes During Basolateral Crawling": https://www.frontiersin.org/articles/10.3389/fimmu.2021.667213/full   TIRF Microscopy Lentiviral transduction was used to generate an endothelial cell line expressing mNeonGreen-Paxillin (derived from addgene plasmid # 129604). Cells were imaged with a Nikon Ti-E microscope equipped with a motorized TIRF Illuminator unit, a 60x TIRF objective (60x Plan Apo, Oil DIC N2, NA =1.49, WD = 120 um) and Perfect Focus System. Images were acquired with an Andor iXon 897 EMCCD camera and the Nikon NIS elements software. mNeonGreen was imaged using the 488 nm laser line and calcein red-orange was imaged using the 561 nm laser line. A quad split dichroic mirror (405 nm, 488 nm, 561 nm, 640 nm) was used in combination with dual band pass emission filter (515 to 545 nm, 600 to 650 nm). To achieve a larger field of view a 3 x 3 tile scans was acquired with 15% overlap stitching on the GFP channel. Time lapse images were taken every 10 s.

opencc-by-4.0Nov 2022View details →

Neutrophil Profiles of Pediatric COVID-19 and Multisystem Inflammatory Syndrome in Children

Code and data for the manuscript "Neutrophil Profiles of Pediatric COVID-19 and Multisystem Inflammatory Syndrome in Children" to be published in Cell Reports Medicine. Contains all code located at <a href="https://github.com/lasalletj/COVID_Neutrophils">https://github.com/lasalletj/</a><a href="https://github.com/lasalletj/Pediatric_COVID_MISC_Neutrophils">Pediatric_COVID_MISC_Neutrophils</a> as well as additional data files needed to run the code and supplementary materials for the manuscript. Any additional information required to reanalyze the data reported in this work paper is available from the Lead Contact, Lael Yonker (lyonker@mgh.harvard.edu) upon request.

opencc-by-4.0Nov 2022View details →

Trapalyzer: A computer program for quantitative analyses in fluorescent live-imaging studies of Neutrophil Extracellular Trap formation.

This data set contains a set of fluorescent microscopy images of a co-culture of neutrophil cells and E. coli bacteria used to study the Neutrophil Extracellular Trap (NET) formation stimulated by bacteria.  NETs and live cells were visualized with a double fluorescent staining of DNA using Hoechst 33342 and SYTOX Green.  Reagents. Roswell Park Memorial Institute (RPMI) 1640 medium, HEPES, SYTOXTM Green, and Hoechst 33342 were purchased from Thermo Fisher Scientific (Waltham, USA). LB broth was purchased from Sigma Aldrich (St Louis, MO, USA). Preparation of blood neutrophils. Neutrophils were obtained from peripheral blood of one healthy blood donor. Blood sample was purchased at Local Blood Donation Centre and according to local regulations, the blood donor enabled blood donation center to sell their blood samples for scientific purposes and the consent of bioethical committee was not required. Blood was collected into a citrate tube and processed within 2 hours from collection. Neutrophils were isolated using density gradient centrifugation followed by polyvinyl alcohol sedimentation, exactly as described in [1]. Isolated neutrophils were suspended in RPMI 1640 medium with 10 mM HEPES (RH).   Preparation of bacteria. Escherichia coli (American Type Culture Collection(ATCC) 25922 strain) were grown overnight in LB broth with shaking. In the morning, an aliquot of bacterial culture was taken, diluted 100 x in a fresh LB medium and grown for subsequent 2-3 hours. Subsequently, bacterial cultures were washed and resuspended in RH medium. Co-culture of neutrophils with bacteria Neutrophils were seeded into the wells of 48-well plates at the density of 2 ⨉ 104 cells/well and allowed to settle for 30 minutes at 37°C, 5% CO2. Subsequently, E. coli was added into the appropriate wells at the multiplicity of infection of 4 or 1 (E.coli: neutrophil). Neutrophils incubated without bacteria were used as a control group. A technical duplicate for each condition was prepared.   For each intended timepoint (t=0, 60, 90, 120, 180 minutes), a separate 48 well plate was prepared. The plates were centrifuged for 5 minutes at 250 g to allow the contact of bacteria with neutrophils. The plates were incubated at 37°C, 5\% CO2 for a specified time and then the samples were stained with SYTOXTM Green (100 nM) and Hoechst 33342 (1.25 μM) for 10 minutes. Four images of each well were taken with Leica DMi8 fluorescent microscope equipped with a 10× magnification objective (Leica, Wetzlar, Germany). Overall, 120 images have been obtained.   2019_04_24--ecoli_neu_tiff_channel_merged.zip: Images in .tif format, each containing 5 channels: channel 1 for SYTOX Green fluorescent stain (green fluorescence), channel 2 for Hoechst 33342 fluorescent stain (blue fluorescence), and three channels for transmission light encoded in RGB values.    2019_04_24--ecoli_neu_tiff_raw_exported.zip: Images split by different light sources: transmission light (_ch00.tif), SYTOX Green fluorescence (_ch01.tif), Hoechst 33342 fluorescence (_ch02.tif).   [1] Bystrzycka W, Moskalik A, Sieczkowska S, Manda-Handzlik A, Demkow U, Ciepiela O. The effect of clindamycin and amoxicillin on neutrophil extracellular trap (NET) release. Cent Eur J Immunol. 2016;41(1):1-5. doi:10.5114/ceji.2016.58811

opencc-by-4.0Aug 2022View details →

Gene expression in monocytes, neutrophils and whole blood after stroke

Dataset from: Carmona-Mora, P., Knepp, B., Jickling, G.C. et al. Monocyte, neutrophil, and whole blood transcriptome dynamics following ischemic stroke. BMC Med 21, 65 (2023). https://doi.org/10.1186/s12916-023-02766-1 All methods available in the publication above. Abstract Background After ischemic stroke (IS), peripheral leukocytes infiltrate the damaged region and modulate the response to injury. Peripheral blood cells display distinctive gene expression signatures post IS and these transcriptional programs reflect changes in immune responses to IS. Dissecting the temporal dynamics of gene expression after IS improves our understanding of immune and clotting responses at the molecular and cellular level that are involved in acute brain injury and may assist with time-targeted, cell-specific therapy. Methods The transcriptomic profiles from peripheral monocytes, neutrophils, and whole blood from 38 ischemic stroke patients and 18 controls were analyzed with RNAseq as a function of time and etiology after stroke. Differential expression analyses were performed at 0-24 h, 24-48 h, and >48 h following stroke. Results Unique patterns of temporal gene expression and pathways were distinguished for monocytes, neutrophils and whole blood with enrichment of interleukin signaling pathways for different timepoints and stroke etiologies. Compared to control subjects, gene expression was generally up-regulated in neutrophils and generally down- regulated in monocytes over all times for cardioembolic, large vessel and small vessel strokes. Self-Organizing Maps identified gene clusters with similar trajectories of gene expression over time for different stroke causes and sample types. Weighted Gene Co- expression Network Analyses identified modules of co-expressed genes that significantly varied with time after stroke and included hub genes of immunoglobulin genes in whole blood. Conclusions Altogether, the identified genes and pathways are critical for understanding how the immune and clotting systems change over time after stroke. This study identifies potential time- and cell-specific biomarkers and treatment targets. clinical_parameters_MON.txt: Clinical parameters from cohort used from monocyte samples. clinical_parameters_NEU.txt: Clinical parameters from cohort used from neutrophil samples. clinical_parameters_WB.txt: Clinical parameters from cohort used from whole blood samples. MON_gene_counts_filtered-WGCNA.txt: Filtered counts of each annotated gene from monocyte samples, cohort used for WGCNA analyses, (TPM normalized, non-log, filtered features where maximum <=40 reads were excluded). NEU_gene_counts_filtered-WGCNA.txt: Filtered counts of each annotated gene from neutrophil samples, cohort used for WGCNA analyses, (TPM normalized, non-log, filtered features where maximum <=40 reads were excluded). WB_gene_counts_filtered-WGCNA.txt: Filtered counts of each annotated gene from whole blood samples, cohort used for WGCNA analyses, (TPM normalized, non-log, filtered features where maximum <=80 reads were excluded). MON_gene_raw_counts.txt: raw counts for cohort used of monocyte samples. NEU_gene_raw_counts.txt: raw counts for cohort used of neutrophil samples. WB_gene_raw_counts.txt: raw counts for cohort used of whole blood samples. MON_Time_Course_filtered_normalized_counts_ready.txt: matrix counts of each annotated gene used for differential expression analyses of time points in monocyte samples. (TPM normalized, filtered features where maximum <=30 reads were excluded). NEU_Time_Course_filtered_normalized_counts_ready.txt: matrix counts of each annotated gene used for differential expression analyses of time points in neutrophil samples. (TPM normalized, filtered features where maximum <=30 reads were excluded). WB_Time_Course_filtered_normalized_counts_ready.txt: matrix counts of each annotated gene used for differential expression analyses of time points in whole blood samples. (TPM normalized, filtered features where maximum <=30 reads were excluded).   All methods to generate the above files are available in the publication: Carmona-Mora, P., Knepp, B., Jickling, G.C. et al. Monocyte, neutrophil, and whole blood transcriptome dynamics following ischemic stroke. BMC Med 21, 65 (2023). https://doi.org/10.1186/s12916-023-02766-1

publicOct 2024View details →

IFN-γ primes bone marrow neutrophils to acquire regulatory functions in severe viral respiratory infections

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publicMay 2024View details →

Data from: Self-extinguishing relay waves enable homeostatic control of human neutrophil swarming

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publicJul 2025View details →

Time course of metabolic variations in human neutrophils with PMA treatment alone or in combination with DPI: Part 1

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publicJul 2025View details →

Metabolic variations in human neutrophils with different combinations of PMA treatments (2DG, 6AN, DPI and AA): Part 2

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opencc-by-4.0Nov 2020View details →

Pretreatment Neutrophil-to-Lymphocyte Ratio, Mutational Load, and Outcomes in Patients Treated with Immune Checkpoint Inhibitors

This dataset has been used to analyze the association between pre-treatment neutrophil-to-lymphocyte ratio and tumour mutational burden with survival and response to treatment in immunotherapy-treated patients with cancer. The dataset contains clinical and genomic data for 2,037 patients with 18 cancer types.

opencc-by-4.0Jul 2017View details →

FACS output files for neutrophils and monocytes

This dataset contains FACS output files of the studies of the apoptotic rate in neutrophils and monocytes under aflotoxin B1 exposure and treatment with Schiff base derivatives. Following groups of animals were studied: CNTRL – intact animals; PLP, PLT and NLT intact animals received 10-day oral treatment with corresponding Schiff bases at 10mg/kg dosage; AFB1 – rats treated with AFB1 for 21 days at 25μg/kg dosage; AFB1+PLP, AFB1+PLT, AFB1+NLT – AFB1 exposed rats treated with corresponding Schiff bases (mycotoxin and Schiff base dosages were similar in all treated groups). AFB1 - aflatoxin B1, PLP, picolinyl-L-phenylalaninate; PLT, picolinyl-L-tryptophanate; NLT, nicotinyl-L-tryptophanate.

opencc-by-4.0Aug 2024View details →

Comparison of Fixed Single Cell RNA-seq Methods to Enable Transcriptome Profiling of Neutrophils in Clinical Samples

Monitoring neutrophil gene expression is a powerful tool for understanding disease mechanisms, developing new diagnostics, therapies and optimizing clinical trials. Neutrophils are sensitive to the processing, storage and transportation steps that are involved in clinical sample analysis. This study is the first to evaluate the capabilities of technologies from 10X Genomics, PARSE Biosciences, and HIVE (Honeycomb Biotechnologies) to generate high-quality RNA data from human blood-derived neutrophils. Our comparative analysis shows that all methods produced high quality data, importantly capturing the transcriptomes of neutrophils. 10X FLEX cell populations in particular showed a close concordance with the flow cytometry data. Here, we establish a reliable single-cell RNA sequencing workflow for neutrophils in clinical trials: we offer guidelines on sample collection to preserve RNA quality and demonstrate how each method performs in capturing sensitive cell populations in clinical practice. This dataset includes the FACS, 10X 3', Parse, 10X Flex, and Hive data and analysis.

opencc-by-4.0Oct 2023View details →

Dataset related to article "Neutrophils mediate protection in colitis and carcinogenesis by controlling bacterial invasion and IL-22 production by gdT cells"

This record contains raw data related to article "Neutrophils mediate protection in colitis and carcinogenesis by controlling bacterial invasion and IL-22 production by gd T cells"AbstractNeutrophils are the most abundant leukocytes in human blood and play a primary role in resistance against invading microorganisms and in the acute inflammatory response. However, their role in colitis and colitis-associated colorectal cancer is still under debate. Therefore, this study aims to dissect the role of neutrophils in these pathological contexts by using a rigorous genetic approach. Neutrophil-deficient mice (Csf3r-/- mice) were challenged with classic models of colitis and colitis-associated colorectal cancer and the role of neutrophils was assessed by histological, cellular and molecular analyses coupled with adoptive cell transfer and correlative analyses using human datasets. Csf3r-/- mice showed increased susceptibility to colitis and colitis-associated colorectal cancer compared to control Csf3r+/+ mice and adoptive transfer of neutrophils in Csf3r-/- mice reverted the phenotype. In colitis, Csf3r-/- mice showed increased bacterial invasion and reduced number of healing ulcers in the colon, indicating compromised regenerative capacity of epithelial cells. Neutrophils were essential for  T cell polarization and IL-22 production. In patients with ulcerative colitis, the expression of CSF3R was positively correlated with IL-22 and IL-23 expression. Moreover, gene signatures associated with epithelial cell development, proliferation and antimicrobial response were enriched in CSF3Rhigh patients. Our data support a model where neutrophils mediate protection against intestinal inflammation and colitis-associated colorectal cancer by controlling the intestinal microbiota and driving the activation of an IL-22-dependent tissue repair pathway.