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Experiment Overview

Repository ID: FR-FCM-ZYTZ Experiment name: CyTOF immune profiling of chikungunya virus infection MIFlowCyt score: 65.47%
Primary researcher: Adeeb Rahman PI/manager: Adeeb Rahman Uploaded by: Adeeb Rahman
Experiment dates: 2014-10-01 - 2016-09-01 Dataset uploaded: Nov 2018 Last updated: Nov 2018
Keywords: [human PBMCs] [mass cytometry] [CyTOF] [infectious disease] [chikungunya] Manuscripts: [30150281] [PMC6110311]
Organizations: Icahn School of Medicine at Mount Sinai , New York, NY (United States of America)
Purpose: The goal of this study was to comprehensively analyze the peripheral immune response to acute chikungunya virus infection. Blood samples were collected as part of a hospital-based study of dengue and chikungunya in the Nicaraguan National Pediatric Reference Hospital in Managua, Nicaragua. The study includes samples collected from a total of 42 pediatric cases with detectable CHIKV viremia presenting to the hospital between November 2014 and October 2015 were included. Paired PBMC samples were collected at acute (1-2 d post symptom onset) and convalescent (15-17 d post symptom onset) infection timepoints for a total of 84 samples. The samples were analyzed by mass cytometry to broadly characterize the immune profile at each timepoint.
Conclusion: We find several associations between immune cell subsets that change in frequency and phenotype between the acute and convalescent phases of infection, most notably monocytes.
Comments: None
Funding: This work was supported by NIH/NIAID grants U19AI118610, R33AI100186 and F30AI122673
Quality control: Paired acute and convalescent samples were barcoded using CD45 antibodies conjugated to distinct isotopes and pooled prior to staining to minimize technical variability during staining and data acquisition.


Experiment variables

Individuals
· 1758 160406_EHA001_1758_1_Patients_Acute.fcs · 160406_EHA001_1758_1_Patients_Conv.fcs
· 1760 160406_EHA001_1760_1_Patients_Acute.fcs · 160406_EHA001_1760_1_Patients_Conv.fcs
· 1773 160406_EHA001_1773_1_Patients_Acute.fcs · 160406_EHA001_1773_1_Patients_Conv.fcs
· 1785 160406_EHA001_1785_1_Patients_Acute.fcs · 160406_EHA001_1785_1_Patients_Conv.fcs
· 1790 160406_EHA001_1790_1_Patients_Acute.fcs · 160406_EHA001_1790_1_Patients_Conv.fcs
· 1793 160406_EHA001_1793_1_Patients_Acute.fcs · 160406_EHA001_1793_1_Patients_Conv.fcs
· 1794 160406_EHA001_1794_1_Patients_Acute.fcs · 160406_EHA001_1794_1_Patients_Conv.fcs
· 1800 160406_EHA001_1800_1_Patients_Acute.fcs · 160406_EHA001_1800_1_Patients_Conv.fcs
· 1802 160406_EHA001_1802_1_Patients_Acute.fcs · 160406_EHA001_1802_1_Patients_Conv.fcs
· 1822 160406_EHA001_1822_1_Patients_Acute.fcs · 160406_EHA001_1822_1_Patients_Conv.fcs
· 1823 160406_EHA001_1823_1_Patients_Acute.fcs · 160406_EHA001_1823_1_Patients_Conv.fcs
· 1824 160406_EHA001_1824_1_Patients_Acute.fcs · 160406_EHA001_1824_1_Patients_Conv.fcs
· 1844 160407_EHA001_1844_1_Patients_Acute.fcs · 160407_EHA001_1844_1_Patients_Conv.fcs
· 1847 160407_EHA001_1847_1_Patients_Acute.fcs · 160407_EHA001_1847_1_Patients_Conv.fcs
· 1862 160408_EHA001_1862_1_Patients_Acute.fcs · 160408_EHA001_1862_1_Patients_Conv.fcs
· 1863 160408_EHA001_1863_1_Patients_Acute.fcs · 160408_EHA001_1863_1_Patients_Conv.fcs
· 1864 160408_EHA001_1864_1_Patients_Acute.fcs · 160408_EHA001_1864_1_Patients_Conv.fcs
· 1878 160408_EHA001_1878_1_Patients_Acute.fcs · 160408_EHA001_1878_1_Patients_Conv.fcs
· 1857 160406_EHA001_1857_1_Patients_Acute.fcs · 160406_EHA001_1857_1_Patients_Conv.fcs
· 1828 160407_EHA001_1828_1_Patients_Acute.fcs · 160407_EHA001_1828_1_Patients_Conv.fcs
· 1829 160407_EHA001_1829_1_Patients_Acute.fcs · 160407_EHA001_1829_1_Patients_Conv.fcs
· 1838 160407_EHA001_1838_1_Patients_Acute.fcs · 160407_EHA001_1838_1_Patients_Conv.fcs
· 1839 160407_EHA001_1839_1_Patients_Acute.fcs · 160407_EHA001_1839_1_Patients_Conv.fcs
· 1842 160407_EHA001_1842_1_Patients_Acute.fcs · 160407_EHA001_1842_1_Patients_Conv.fcs
· 1879 160408_EHA001_1879_1_Patients_Acute.fcs · 160408_EHA001_1879_1_Patients_Conv.fcs
· 1880 160408_EHA001_1880_1_Patients_Acute.fcs · 160408_EHA001_1880_1_Patients_Conv.fcs
· 1882 160408_EHA001_1882_1_Patients_Acute.fcs · 160408_EHA001_1882_1_Patients_Conv.fcs
· 1885 160408_EHA001_1885_1_Patients_Acute.fcs · 160408_EHA001_1885_1_Patients_Conv.fcs
· 1886 160408_EHA001_1886_1_Patients_Acute.fcs · 160408_EHA001_1886_1_Patients_Conv.fcs
· 1889 160408_EHA001_1889_1_Patients_Acute.fcs · 160408_EHA001_1889_1_Patients_Conv.fcs
· 1890 160408_EHA001_1890_1_Patients_Acute.fcs · 160408_EHA001_1890_1_Patients_Conv.fcs
· 1891 160408_EHA001_1891_1_Patients_Acute.fcs · 160408_EHA001_1891_1_Patients_Conv.fcs
· 1897 160408_EHA001_1897_1_Patients_Acute.fcs · 160408_EHA001_1897_1_Patients_Conv.fcs
· 1910 160408_EHA001_1910_1_Patients_Acute.fcs · 160408_EHA001_1910_1_Patients_Conv.fcs
· 1912 160408_EHA001_1912_1_Patients_Acute.fcs · 160408_EHA001_1912_1_Patients_Conv.fcs
· 1914 160408_EHA001_1914_1_Patients_Acute.fcs · 160408_EHA001_1914_1_Patients_Conv.fcs
· 1778 160406_EHA001_1778_1_Patients_Conv.fcs
· 1918 160408_EHA001_1918_1_Patients_Acute.fcs · 160408_EHA001_1918_1_Patients_Conv.fcs
· 1920 160408_EHA001_1920_1_Patients_Acute.fcs · 160408_EHA001_1920_1_Patients_Conv.fcs
· 1924 160408_EHA001_1924_1_Patients_Acute.fcs · 160408_EHA001_1924_1_Patients_Conv.fcs
· 1937 160408_EHA001_1937_1_Patients_Acute.fcs · 160408_EHA001_1937_1_Patients_Conv.fcs
· 1925 160411_EHA001_1925_1_Patients_Acute.fcs · 160411_EHA001_1925_1_Patients_Conv.fcs
· 1938 160411_EHA001_1938_1_Patients_Acute.fcs · 160411_EHA001_1938_1_Patients_Conv.fcs
· 1948 160411_EHA001_1948_1_Patients_Acute.fcs · 160411_EHA001_1948_1_Patients_Conv.fcs

Timepoints
· Acute 160406_EHA001_1758_1_Patients_Acute.fcs · 160406_EHA001_1760_1_Patients_Acute.fcs · 160406_EHA001_1773_1_Patients_Acute.fcs · 160406_EHA001_1785_1_Patients_Acute.fcs · 160406_EHA001_1790_1_Patients_Acute.fcs · 160406_EHA001_1793_1_Patients_Acute.fcs · 160406_EHA001_1794_1_Patients_Acute.fcs · 160406_EHA001_1800_1_Patients_Acute.fcs · 160406_EHA001_1802_1_Patients_Acute.fcs · 160406_EHA001_1822_1_Patients_Acute.fcs · 160406_EHA001_1823_1_Patients_Acute.fcs · 160406_EHA001_1824_1_Patients_Acute.fcs · 160406_EHA001_1857_1_Patients_Acute.fcs · 160407_EHA001_1828_1_Patients_Acute.fcs · 160407_EHA001_1829_1_Patients_Acute.fcs · 160407_EHA001_1838_1_Patients_Acute.fcs · 160407_EHA001_1839_1_Patients_Acute.fcs · 160407_EHA001_1842_1_Patients_Acute.fcs · 160407_EHA001_1844_1_Patients_Acute.fcs · 160407_EHA001_1847_1_Patients_Acute.fcs · 160408_EHA001_1862_1_Patients_Acute.fcs · 160408_EHA001_1863_1_Patients_Acute.fcs · 160408_EHA001_1864_1_Patients_Acute.fcs · 160408_EHA001_1878_1_Patients_Acute.fcs · 160408_EHA001_1879_1_Patients_Acute.fcs · 160408_EHA001_1880_1_Patients_Acute.fcs · 160408_EHA001_1882_1_Patients_Acute.fcs · 160408_EHA001_1885_1_Patients_Acute.fcs · 160408_EHA001_1886_1_Patients_Acute.fcs · 160408_EHA001_1889_1_Patients_Acute.fcs · 160408_EHA001_1890_1_Patients_Acute.fcs · 160408_EHA001_1891_1_Patients_Acute.fcs · 160408_EHA001_1897_1_Patients_Acute.fcs · 160408_EHA001_1910_1_Patients_Acute.fcs · 160408_EHA001_1912_1_Patients_Acute.fcs · 160408_EHA001_1914_1_Patients_Acute.fcs · 160408_EHA001_1918_1_Patients_Acute.fcs · 160408_EHA001_1920_1_Patients_Acute.fcs · 160408_EHA001_1924_1_Patients_Acute.fcs · 160408_EHA001_1937_1_Patients_Acute.fcs · 160411_EHA001_1925_1_Patients_Acute.fcs · 160411_EHA001_1938_1_Patients_Acute.fcs · 160411_EHA001_1948_1_Patients_Acute.fcs
· Convalescent 160406_EHA001_1778_1_Patients_Conv.fcs · 160406_EHA001_1758_1_Patients_Conv.fcs · 160406_EHA001_1760_1_Patients_Conv.fcs · 160406_EHA001_1773_1_Patients_Conv.fcs · 160406_EHA001_1785_1_Patients_Conv.fcs · 160406_EHA001_1790_1_Patients_Conv.fcs · 160406_EHA001_1793_1_Patients_Conv.fcs · 160406_EHA001_1794_1_Patients_Conv.fcs · 160406_EHA001_1800_1_Patients_Conv.fcs · 160406_EHA001_1802_1_Patients_Conv.fcs · 160406_EHA001_1822_1_Patients_Conv.fcs · 160406_EHA001_1823_1_Patients_Conv.fcs · 160406_EHA001_1824_1_Patients_Conv.fcs · 160406_EHA001_1857_1_Patients_Conv.fcs · 160407_EHA001_1828_1_Patients_Conv.fcs · 160407_EHA001_1829_1_Patients_Conv.fcs · 160407_EHA001_1838_1_Patients_Conv.fcs · 160407_EHA001_1839_1_Patients_Conv.fcs · 160407_EHA001_1842_1_Patients_Conv.fcs · 160407_EHA001_1844_1_Patients_Conv.fcs · 160407_EHA001_1847_1_Patients_Conv.fcs · 160408_EHA001_1862_1_Patients_Conv.fcs · 160408_EHA001_1863_1_Patients_Conv.fcs · 160408_EHA001_1864_1_Patients_Conv.fcs · 160408_EHA001_1878_1_Patients_Conv.fcs · 160408_EHA001_1879_1_Patients_Conv.fcs · 160408_EHA001_1880_1_Patients_Conv.fcs · 160408_EHA001_1882_1_Patients_Conv.fcs · 160408_EHA001_1885_1_Patients_Conv.fcs · 160408_EHA001_1886_1_Patients_Conv.fcs · 160408_EHA001_1889_1_Patients_Conv.fcs · 160408_EHA001_1890_1_Patients_Conv.fcs · 160408_EHA001_1891_1_Patients_Conv.fcs · 160408_EHA001_1897_1_Patients_Conv.fcs · 160408_EHA001_1910_1_Patients_Conv.fcs · 160408_EHA001_1912_1_Patients_Conv.fcs · 160408_EHA001_1914_1_Patients_Conv.fcs · 160408_EHA001_1918_1_Patients_Conv.fcs · 160408_EHA001_1920_1_Patients_Conv.fcs · 160408_EHA001_1924_1_Patients_Conv.fcs · 160408_EHA001_1937_1_Patients_Conv.fcs · 160411_EHA001_1925_1_Patients_Conv.fcs · 160411_EHA001_1938_1_Patients_Conv.fcs · 160411_EHA001_1948_1_Patients_Conv.fcs

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