This Yu_et_al_2017-PLOS_ONE-TB_Gene_Expression_Data-ReadMe.txt file was generated on September 22, 2017 by Elaine Yu. Updated December 4, 2017 with publication citation information by Wendy Kozlowski by request of the author (Yu). ------------------- GENERAL INFORMATION ------------------- 1. Title of Dataset Data from "Host transcriptional responses following ex vivo re-challenge with Mycobacterium tuberculosis vary with disease status" 2. Author Information Elaine A. Yu, Serene H. John, Elizabeth C. Tablante, Christine A. King, John Kenneth, David G. Russell, Saurabh Mehta Principal Investigator Contact Information Name: Saurabh Mehta Institution: Cornell University, Division of Nutritional Sciences Address: 314 Savage Hall; Ithaca NY 14853 Email: smehta@cornell.edu 3. Date of data collection 2012-2013 4. Geographic location of data collection Bangalore, Karnataka, India 5. Information about funding sources that supported the collection of the data Research reported in this publication was supported by the National Institutes of Health (National Institute of Diabetes and Digestive and Kidney Diseases; T32-DK007158 award); the Mario Einaudi Center for International Studies (South Asia Program), Human Ecology Alumni Association, Graduate School, Division of Nutritional Sciences at Cornell University (for E.A.Y. research and travel support). D.G.R. is supported by National Institutes of Health (National Institute of Allergy and Infectious Diseases; AI118582 award). The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institute of Diabetes and Digestive and Kidney Diseases, National Institute of Allergy and Infectious Diseases, or the National Institutes of Health. -------------------------- SHARING/ACCESS INFORMATION -------------------------- 1. Licenses/restrictions placed on the data: Creative Commons Attribution (CC BY) 4.0 International 2. Links to publications that cite or use the data: Yu EA, John SH, Tablante EC, King CA, Kenneth J, et al. (2017) Host transcriptional responses following ex vivo re-challenge with Mycobacterium tuberculosis vary with disease status. PLOS ONE 12(10): e0185640. https://doi.org/10.1371/journal.pone.0185640 3. Recommended citation for the data: Yu EA, John SH, Tablante EC, King CA, Kenneth J, Russell DG, Mehta S. 2017. Data from "Host transcriptional responses following ex vivo re-challenge with Mycobacterium tuberculosis vary with disease status”. Available from Cornell University eCommons Data Repository [Internet]. DOI:10.7298/X4JH3JBN. --------------------- DATA & FILE OVERVIEW --------------------- 1. File List A. Filename: Yu_et_al_2017_PLOS_ONE_TB_Gene_Expression_Data.csv Short description: Relative gene expression data among patients in four subgroups (active tuberculosis disease, latent tuberculosis infection, previous active tuberculosis disease and successful treatment, healthy controls), after ex vivo Mycobacterium tuberculosis infection. 2. Are there multiple versions of the dataset? No -------------------------- METHODOLOGICAL INFORMATION -------------------------- 1. Description of methods used for collection/generation of data: We evaluated gene expression profiles from peripheral blood mononuclear cells following ex vivo challenge with Mycobacterium tuberculosis, among participants with active TB disease (ATBD, n=10), latent TB infection (LTBI, n=10), and previous active TB disease (after successful treatment; PTBD, n=10), relative to controls (n=10). Differential gene expression profiles were assessed by suppression-subtractive hybridization, dot blot, real-time polymerase chain reaction, and the comparative cycle threshold methods. 2. Methods for processing the data: Relative gene expression was reported as fold-change, based on the comparative cycle threshold (2-CT) method with human acidic ribosomal protein (HUPO) as the internal control gene. For each comparison, fold-change was reported as the average of the fold-changes of the two replicates. ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: Yu_et_al_2017_PLOS_ONE_TB_Gene_Expression_Data.csv ----------------------------------------- 1. Number of variables: 17 2. Number of rows: 14 3. Variable List A. Name: Gene Description: Genes identified through the suppression-subtractive hybridization and dot blot methods. B. Name: ATB Description: Active tuberculosis disease (Group 1; replicate 1), cycle threshold values. C. Name: ATBHUPO Description: Human acidic ribosomal protein (HUPO) as the internal control gene for active tuberculosis disease (Group 1; replicate 1), cycle threshold values. D. Name: LTB Description: Latent tuberculosis infection (Group 2; replicate 1), cycle threshold values. E. Name: LTBHUPO Description: Human acidic ribosomal protein (HUPO) as the internal control gene for latent tuberculosis infection (Group 2; replicate 1), cycle threshold values. F. Name: CTB Description: Previous active tuberculosis disease with successful treatment (Group 3; replicate 1), cycle threshold values. G. Name: CTBHUPO Description: Human acidic ribosomal protein (HUPO) as the internal control gene for previous active tuberculosis disease with successful treatment (Group 3; replicate 1), cycle threshold values. H. Name: HC Description: Healthy controls (Group 4; replicate 1), cycle threshold values. I. Name: HCHUPO Description: Human acidic ribosomal protein (HUPO) as the internal control gene for healthy controls (Group 4; replicate 1), cycle threshold values. J. Name: ATB2 Description: Active tuberculosis disease (Group 1; replicate 2), cycle threshold values. K. Name: ATBHUPO2 Description: Human acidic ribosomal protein (HUPO) as the internal control gene for active tuberculosis disease (Group 1; replicate 2), cycle threshold values. L. Name: LTB2 Description: Latent tuberculosis infection (Group 2; replicate 2), cycle threshold values. M. Name: LTBHUPO2 Description: Human acidic ribosomal protein (HUPO) as the internal control gene for latent tuberculosis infection (Group 2; replicate 2), cycle threshold values. N. Name: CTB2 Description: Previous active tuberculosis disease with successful treatment (Group 3; replicate 2), cycle threshold values. O. Name: CTBHUPO2 Description: Human acidic ribosomal protein (HUPO) as the internal control gene for previous active tuberculosis disease with successful treatment (Group 3; replicate 2), cycle threshold values. P. Name: HC2 Description: Healthy controls (Group 4; replicate 2), cycle threshold values. Q. Name: HCHUPO2 Description: Human acidic ribosomal protein (HUPO) as the internal control gene for healthy controls (Group 4; replicate 2), cycle threshold values. 4. Missing data codes: Not applicable 5. Specialized formats of other abbreviations used: Active TB disease (ATBD) Chemokine (C-X-C motif) ligand (CXCL) Cluster of differentiation (CD) Ferritin light chain (FTL) Gamma-interferon-inducible protein (IP30) Interleukin (IL) Latent TB infection (LTBI) Mitogen activated protein kinase kinase (MAP2K) Macrophage inflammatory protein (MIP) Monocyte chemotactic protein (MCP) Previous active TB disease (PTBD; after successful treatment) Ras-related nuclear protein (RAN)