Replication Data for: Induction of an early IFN-γ cellular response and high plasma levels of SDF-1α are inversely associated with COVID-19 severity and residence in rural areas in Kenyan patients

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Replication Data for: Induction of an early IFN-γ cellular response and high plasma levels of SDF-1α are inversely associated with COVID-19 severity and residence in rural areas in Kenyan patients
Wanjiku, Perpetual; Orindi, Benedict; Kimotho, John; Sayed, Shahin; Shah, Reena; Saleh Mansoor; Mwacharo, Jedidah; Maronga, Christopher; Oluoch, Vivian; Karanu, Ann; Shah, Jasmit; Nneka, Zaitun; Ochola-Oyier, Lynette Isabella; Abdi, Abdirahman I.; Dunachie, Susanna; Bejon, Philip; Nduati, Eunice; Ndungu, Francis M., 2024, "Replication Data for: Induction of an early IFN-γ cellular response and high plasma levels of SDF-1α are inversely associated with COVID-19 severity and residence in rural areas in Kenyan patients", https://doi.org/10.7910/DVN/XMTCTW, Harvard Dataverse, V1, UNF:6:JkMDcIXMDJ5GzzCjZ4ra3A== [fileUNF]
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Description

This is a replication dataset for the manuscript titled: "Induction of an early IFN-γ cellular response and high plasma levels of SDF-1α are inversely associated with COVID-19 severity and residence in rural areas in Kenyan patients" submitted to the PLOS One journal.

The first dataset describes the baseline characteristics of the Kenyan COVID-19 patients, who were included in this analysis, they were recruited from June 2020 to February 2022. Plasma samples were then collected longitudinally over four successive time points within one month of COVID-19 diagnosis. Dataset contains clinical data on underlying conditions and hospital admission of the patients collected during patient care/treatment. Datasets is shared as .CSV Excel files.

The second dataset contains concentrations of cytokines and chemokines assayed on plasma samples using Luminex assay. Datasets is shared as .CSV Excel files.

The third dataset comprises a subset of 59 patients derived from the second dataset who had at least PBMC samples from 3 timepoints. It contains IFNy secreting cell responses assayed by Elispot for 172 samples. Datasets is shared as .CSV Excel files.

Subject Medicine, Health and Life Sciences
Keyword COVID-19, SARS-CoV-2, IFN-γ-secreting cells, cytokines, chemokines, kinetics, Sub-Saharan Africa
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CC BY 4.0

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PWanjiku_ImmunoCov_data_dictionary_2024.pdf
PWanjiku_ImmunoCov_data_dictionary_2024.pdf
Adobe PDF - 250.6 KB
Published Dec 13, 2024
3 Downloads
MD5: 3e787e892767c373305f666799be4d60
DocumentationVariable Codebook/Data Dictionary
Preview "PWanjiku_ImmunoCov_data_dictionary_2024.pdf"
readme_ImmunoCoV.txt
Plain Text - 7.0 KB
Published Dec 13, 2024
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MD5: d7e54b7796f13d61209fb50b41bee75d
DocumentationReadme
Preview "readme_ImmunoCoV.txt"
baseline_xtcis_data_anon.tab
Tabular Data - 44.7 KB
Published Dec 13, 2024
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19 Variables, 400 Observations UNF:6:hCrYukyBkznb7F/2G7z0Fw==
Patients baseline characteristics
Datacsv file
elispot_data_anon.tab
Tabular Data - 240.8 KB
Published Dec 13, 2024
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173 Variables, 172 Observations UNF:6:AGxC568zK4YC0AM8fKJEqw==
Contains IFNy secreting cell responses for a subset of 59 patients
Datacsv file
Luminex_data.tab
Tabular Data - 84.5 KB
Published Dec 13, 2024
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34 Variables, 400 Observations UNF:6:h1PkUwtuhJX1SUMLzi6hhg==
cytokines and chemokines concentrations
Datacsv file
baseline xtics_dataanalysis.R
R Syntax - 2.1 KB
Published Dec 13, 2024
8 Downloads
MD5: 8a908530310e7d5c3670a8e5719abb70
contains statistical codes of analysis for creating Table 1. Participant demographic and clinical characteristics.
CodeR script
Preview "baseline xtics_dataanalysis.R"
ELISpot_dataanalysis.prism
Unknown - 1.6 MB
Published Dec 13, 2024
3 Downloads
MD5: 963315162a7f9fac8e6cb0e732e82018
LISpot_dataanalysis- Contains statistical analysis for Elispot_data
CodeGraphPad prism file (.pfzx)
luminex_dataanalysis.R
R Syntax - 18.4 KB
Published Dec 13, 2024
5 Downloads
MD5: 4e05d0eaf302f8611333630d6a26a745
Contains statistical codes for analysing Luminex data.
CodeR script
Preview "luminex_dataanalysis.R"
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