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)
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| 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 |
