?This codebook.txt file was generated on 20190128 by Skinner,Pamela ------------------------------------ GENERAL INFORMATION ------------------------------------ 1. Title of Dataset Data from manuscript “Low levels of SIV-specific CD8+ T cells in germinal centers characterizes acute SIV infection” 2. Author Information Name: Pam Skinner Institution: UMN Address: 1971 Commonwealth Ave, St. Paul, MN 55108 Email: skinn002@umn.edu 3. Date of data collection 2015-2018 4. Geographic location of data collection (where was data collected?): University of Minnesota, St. Paul, Minnesota, USA 5. Information about funding sources that supported the collection of the data: This work was supported by a Public Health Service grant from the National Institutes of Health (grant R01AI096966), by Wisconsin National Primate Research Center grant P51OD011106/P51RR000167, by the Wisconsin National Primate Research Center Pathology and Scientific Protocol Implementation Units, NIH Tetramer Core Facility (contract HHSN272201300006C), by the NIH Nonhuman Primate Reagent Resource (grant R24 RR016001), and by the National Institute of Allergy and Infectious Diseases (contract HHSN 2722000900037C). ------------------------------------------------- SHARING/ACCESS INFORMATION ------------------------------------------------- 1. Licenses/restrictions placed on the data: https://creativecommons.org/publicdomain/zero/1.0/ 2. Links to publications that cite or use the data: Shengbin Li, Joy M. Folkvord, Katalin J Kovacs, Reece K. Wagstaff, Gwantwa Mwakalundwa, Aaron K. Rendahl, Eva G. Rakasz, Elizabeth Connick 2 and Pamela J.Skinner. (in press). Low levels of SIV-specific CD8+ T cells in germinal centers characterizes acute SIV infection. PLOS Pathogens. 3. Recommended citation for the data: Skinner, Pamela J. (2018). Data from manuscript entitled "Low levels of SIV-specific CD8+ T cells in germinal centers characterizes acute SIV infection". Retrieved from the Data Repository for the University of Minnesota, http://hdl.handle.net/11299/201327. ------------------------------------ DATA & FILE OVERVIEW ------------------------------------ 1. File List A. Filename: DataFrom_F SIV-specific CD8 T cells_early infection2018.csv Short description: These data contain viral loads, CD4 T cell counts, and quantitative image analysis findings from SIV infected rhesus macaques. --------------------------------------------------- METHODOLOGICAL INFORMATION --------------------------------------------------- 1. Description of methods used for collection/generation of data: Tissues were collected from animals in early SIV infection, and in situ tetramer staining combined with immunohistochemistry was performed on lymph tissue specimens. Quantitative image analysis was performed using ImageJ software. Next, in situ hybridization for SIV RNA and immunohistochemistry staining were performed on the same tissue. All statistical calculations performed in R 3.4.3 Ethics statement: All rhesus macaques used in this study were cared for by the staff at the Wisconsin National Primate Research Center (WNPRC) in accordance with the principles described in the National Research Council's Guide for the Care and Use of Laboratory Animals and with the recommendations of the Weatherall report (https://royalsociety.org/topics-policy/publications/2006/weatherall-report/). This study was approved by the University of Wisconsin-Madison Graduate School Institutional Animal Care and Use Committee (Animal Care and Use Protocol Number G005529). 2. Additional people involved with sample collection, processing, analysis and/or submission: Eva Rakasz and Shengbin Li -------------------------------------------------------------------------------------------------------- DATA-SPECIFIC INFORMATION FOR: DataFrom_F SIV-specific CD8 T cells_early infection2018.csv --------------------------------------------------------------------------------------------------------- 1. Number of variables: 29 2. Number of cases/rows: 18 3. Missing data codes: Blank cell; Data not collected 4. Variable List log10 copies/ml RNA Plasma viral load cells/ul CD4 CD4 T cell counts Tetramer+ cells/mm2 GC Levels of tetramer+ cells in lymph node germinal centers Tetramer+ cells/mm2 F Levels of tetramer+ cells in lymph node follicles Tetramer+ cells/mm2 EF Levels of tetramer+ cells in lymph node extrafollicular areas Tetramer+ cells/mm2 F_EF Follicular to extrafollicular ratios of tetramer+ cells vRNA Cells/mm2 F Levels of SIV viral RNA+ cells in follicles vRNA Cells/mm2 EF Levels of SIV viral RNA+ cells in extrafollicular areas FoxP3 cells/mm2 F Levels of FoxP3 cells in follicles FoxP3 cells/mm2 EF Levels of FoxP3 cells in extrafollicular areas % Tetramer+ cells PD-1+ F Levels of PD-1+ cells in follicles % Tetramer+ cells PD-1+ EF Levels of PD-1+ cells in extrafollicular areas % Tetramer+ cells Ki67+ F Levels of Ki67+ cells in follicles % Tetramer+ cells Ki67+ EF Levels of Ki67+ cells in extrafollicular areas Percentages of different types of perf+ cells among tet+ cells inside Follicles Total number of tet+ cells inside follicle % of tet+perf+ cells among all tet+ cells % of tet+perf- cells among all tet+ cells % of perforin high cells among tet+ cells % of perforin medium cells among tet+ cells % of perforin low cells among tet+ cells These data describe the perforin phenotype of tetramer+ cells within lymph node follicles Percentages of different types of perf+ cells among tet+ cells in T Zones Total number of tet+ cells in T Zones % tet+perf+ cells among all tet+ cells % tet+perf- cells among all tet+ cells % of perforin high cells among tet+ cells % of perforin medium cells among tet+ cells % of perforin low cells among tet+ cells These data describe the perforin phenotype of tetramer+ cells within extrafollicular areas of lymph nodes