READ ME File For 'Dataset for Investigating lipid-responsive T cells in tuberculosis; paving the way for new lipidbased vaccines' Dataset DOI: https://doi.org/10.5258/SOTON/D1977 ReadMe Author: Jennie Gullick, University of Southampton ORCID ID 0000-0002-3612-1926 This dataset supports the thesis entitled 'Investigating lipid-responsive T cells in tuberculosis; paving the way for new lipidbased vaccines' AWARDED BY: Univeristy of Southampton DATE OF AWARD: [2021] DESCRIPTION OF THE DATA This dataset contains: Frequency data generated using Flowjo following the analysis of Jurkat cells expressing cloned gamma delta TCRs and acquired by flow cytometry, and also contains Relative Light Unit of Luminescence data recorded by a GloMax Discovery. 'gdTCR Activation - CD69 CD3 T2 Percentage change' contains the calculated percentage change of gdTCR Jurkat cells expressing CD69 or CD3 following stimulation with T2 cells expressing/not expressing CD1c. 'gdTCR Activation - Luciferase T2 Percentage change' contains the calculated percentage change of the luminescence expressed by gdTCR Jurkat cells following stimulation with T2 cells expressing/not expressing CD1c. 'gdTCR Activation - Luciferase THP1 Percentage change' contains the calculated percentage change of the luminescence expressed by gdTCR Jurkat cells following stimulation with THP1 cells expressing/not expressing CD1c. 'gdTCR Activation - Luciferase THP1' contains the relative light units of luminescence expressed by gdTCR Jurkat cells following stimulation with THP1 cells expressing/not expressing CD1c. Frequency data generated using Flowjo following the analysis of cells acquired by flow cytometry. 'Mutant tetramers' contains frequency data related to the percentage of mutant CD1c tetramers that bound the NM4 TCR expressing Jurkat cells. 'Plate bound CD1c Activation Optimisation' contains the frequency of CD69 and CD3 expressing by NM4 TCR expressing Jurkat T cells following incubation with plate-bound CD1c. 'T2-Jurkat Activation Optimisation - CD3' contains the frequency of CD3 expression by NM4 TCR expressing Jurkat T cells following co-culture with T2 cells with or without expression of CD1c. 'T2-Jurkat Activation Optimisation - CD69' contains the frequency of CD69 expression by NM4 TCR expressing Jurkat T cells following co-culture with T2 cells with or without expression of CD1c. 'Vd1 expansion' contains the frequency of Vd1 T cells in PBMC samples over time following culture with plate-bound anti-gdTCR antibody 'Vd1 expansion with CD1c' contains the frequency of Vd1 T cells in PBMC samples over time following culture with plate-bound anti-gdTCR antibody and CD1c 'AIM - Co-receptor Activation Markers TB Status' contains frequency data of expanded T cells displaying CD4 and CD8 co-receptors and CD69, CD137 and CD25 activation markers. Donors separated by TB status. 'AIM - Co-receptor Activation Markers' contains frequency data of expanded T cells displaying CD4 and CD8 co-receptors and CD69, CD137 and CD25 activation markers. 'AIM - Co-receptor Pie Charts'contains frequency data in pie charts of the co-receptor expression of expanded T cells by different donors 'AIM - Expansion + Activation'contains frequency data of the expansion of different T cell subsets and their activation status TIFF file images of Immunohistochemical staining of lung sections taken from TB patients and control subjects acquired by a DotSlide microscope. Tissue sections from each donor were stained with anti-CD1c and anti-TCRd antibodies. PBMC and Lung samples were acquired from TB patients and uninfected control subjects and were analysed for their T cell subsets and reactivity to CD1c tetramers 'TB Data 1st Cohort - HIV T cell subsets' contains frequency data on T cell subsets from patients separated by HIV status 'TB Data 1st Cohort - HIV Tetramer+ T cell subsets' contains frequency data on T cell subsets from patients separated by HIV status that react to the CD1c tetramer 'TB Data 1st Cohort - T cell subsets' contains frequency data on T cell subsets from each patient 'TB Data 1st Cohort - Tetramer + T cell subsets' contains frequency data on T cell subsets from each patient reactive to CD1c tetramers 'TB Data 2nd Cohort - CD69CD103 T cell subsets' contains frequency data on T cell subsets from each patient in the second cohort that are CD69+CD103+ 'TB Data 2nd Cohort - Lung PD1 T cell subsets' contains frequency data on PD1 expression by T cell subsets in the lung from each patient in the second cohort 'TB Data 2nd Cohort - Lung T cell subsets' contains frequency data on T cell subsets in the lung from each patient in the second cohort 'TB Data 2nd Cohort - Lung Tetramer+ T cell subsets' contains frequency data on T cell subsets in the lung from each patient in the second cohort that react to the CD1c tetramer 'TB Data 2nd Cohort - Matched PD1 T cell subsets' contains frequency data on PD1 expression by T cell subsets in matched PBMC and Lung samples from each patient in the second cohort 'TB Data 2nd Cohort - Matched T cell subsets' contains frequency data on T cell subsets in matched PBMC and Lung samples from each patient in the second cohort 'TB Data 2nd Cohort - Matched Tetramer+ T cell subsets' contains frequency data on T cell subsets in matched PBMC and Lung samples from each patient in the second cohort that react to the CD1c tetramer 'TB Data 2nd Cohort - PBMC T cell subsets' contains frequency data on T cell subsets in PBMC samples from each patient in the second cohort 'Ex vivo + Lung + Expansion iNKT' detailing the frequency of iNKT cells in the circulation of M.tb challenged macaques, in biopsied lung lobes following necropsy, and the frequency of expanded iNKTs following agonistic stimulation. 'mCD1c-pET23d' contains the vector map of the macaque ortholog of CD1c that was cloned into the pET23d vector for expression as inclusion bodies. Graphpad Prism and Snapgene Viewer are required to view this data Date of data collection: [January 2018 - March 2021] Information about geographic location of data collection: Southampton General Hospital, Southampton, UK. Africa Health Research Institute, Durban, South Africa. Public Health England, Porton Down, UK. Date that the file was created: September 2021