Computational protocol: Impaired T Cell Responsiveness to Interleukin-6 in Hematological Patients with Invasive Aspergillosis

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Protocol publication

[…] At least 10,000 gated events were collected for each sample. Singlet events were acquired based on forward scatter and side scatter properties ( and Figs). Potential blast cells were excluded at the time of analysis by gating on CD45 high cells ( and Figs). Dead cells were excluded on the basis of forward scatter and side scatter properties and/or live/dead stain. Cells were acquired on an LSR II instrument (BD Immunocytometry Systems, San Jose, CA) and analyzed using FlowJo analytical software (Tree star, Version 9.0.2; Ashland, OR). [...] Data was analyzed using GraphPad Prism (GraphPad Software, Inc., Version 6.0; San Diego, CA) and IBM SPSS Statistics (IBM Corp, Version 20.0: Armonk, NY). Heat maps were constructed using CIMminer available at: (Genomics and Bioinformatics Group, Center for Cancer Research (CCR) National Cancer Institute (NCI); Bethesda, MD). Linear regressions were completed using GraphPad via least-squares fit. When analyzing phospho-specific flow data, fold change was calculated by dividing the median fluorescence intensity (MFI) of the stimulated sample by that of the unstimulated sample. For immunoassay data, fold change was calculated by dividing the cytokine levels produced in response to stimulation by those of non-stimulated cells; or, when indicated, by dividing the cytokine levels produced in response to Aspergillus in the presence of IL-6 by those of cells simulated with Aspergillus lysate alone. Detectable Aspergillus-induced cytokine production was defined as >2.5 fold change from baseline. Values ≥ 3 SD were excluded from the data analysis. Statistical significance was determined using unpaired and paired Student’s t-tests, as well as Pearson’s Chi-Square Test. The threshold of statistical significance was defined as p < 0.05. […]

Pipeline specifications

Software tools FlowJo, SPSS
Applications Miscellaneous, Flow cytometry
Organisms Homo sapiens
Diseases Mucormycosis, Mycoses, Hematologic Neoplasms