This readme.txt file was generated on 20160229 by Zhuozhi Huang and updated on 20160916 by Valerie Collins 20160916 UPDATE Final versions of the data were uploaded to DRUM, and the dataset versioned. The "clinical.txt" file was replaced by "clinical.csv," and "FPKMs.txt" and "FPKMs.csv" were replaced by "FPKMs.csv." The original dataset is still available in DRUM at http://hdl.handle.net/11299/177631.1 GENERAL INFORMATION 1. Title of Dataset: Differentially Expressed Gene Transcripts Using RNA Sequencing from the Blood of Immunosuppressed Kidney Allograft Recipients 2. File Information: A. Filename: clinical.txt B. Short description: Clinical Co-variates C. Filename: FPKMs.txt D. Short description: FPKM from RNA Sequencing of Patients (.txt) E. Filename: FPKMs.csv F. Short description: FPKM from RNA Sequencing of Patients (.csv) 3. Principal Investigator Contact Information A. Name: Dorr, Casey B. Institution: University of Minnesota C. Email: dorr0022@umn.edu 4. Associate or Co-investigator Contact Information A. Name: Wu, Baolin B. Institution: University of Minnesota C. Email: baolin@umn.edu 5. Associate or Co-investigator Contact Information A. Name: Guan, Weihua B. Institution: University of Minnesota C. Email: wguan@umn.edu 6. Associate or Co-investigator Contact Information A. Name: Muthusamy, Amutha B. Institution: Minneapolis Medical Research Foundation 7. Associate or Co-investigator Contact Information A. Name: Sanghavi, Kinjal B. Institution: University of Minnesota C. Email: sangh018@umn.edu 8. Associate or Co-investigator Contact Information A. Name: Schladt, David B. Institution: Minneapolis Medical Research Foundation 9. Associate or Co-investigator Contact Information A. Name: Maltzman, Jonathan B. Institution: University of Pennsylvania 10. Associate or Co-investigator Contact Information A. Name: Scherer, Steven B. Institution: Baylor College of Medicine 11. Associate or Co-investigator Contact Information A. Name: Brott, Marcia B. Institution: University of Minnesota C. Email: brott001@umn.edu 12. Associate or Co-investigator Contact Information A. Name: Matas, Arthur B. Institution: University of Minnesota C. Email: matas001@umn.edu 13. Associate or Co-investigator Contact Information A. Name: Jacobson, Pamala B. Institution: University of Minnesota C. Email: jacob117@umn.edu 14. Associate or Co-investigator Contact Information A. Name: Oetting, William B. Institution: University of Minnesota C. Email: oetti001@umn.edu 15. Associate or Co-investigator Contact Information A. Name: Israni, Ajay B. Institution: University of Minnesota C. Email: isran001@umn.edu 16. Date files were created: 20160229 17. Are there multiple versions of the dataset? no 18. Information about funding sources that supported the collection of the data: Sponsorship: This study was funded by National Institute for General Medical Science' Pharmacogenomics Research Network for the project titled "Precision Immune Suppression. The PRECISE Study. Genomics of Transplantation" that was awarded to Pamala A. Jacobson and Baylor College of Medicine Human Genome Sequencing Center. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. METHODOLOGICAL INFORMATION 1. Description of methods used for collection/generation of data: We used the R software (version 3.2.3) to process and output the data into a tab delimited txt file ("FPKMs.txt"), which can be very easily loaded into most analysis software. DATA-SPECIFIC INFORMATION 1. Column headings and paramters in "clinical.txt" A. Full name: ID B. Description: Sample ID C. Units of measurement: n/a D. Full name: Month E. Definition: time when the blood sample is taken. 0 means that the sample was taken pre-transplant and prior to initiation of immune suppressant therapy. F. Unites of measurement: month G. Full name: SID H. Definition: Specimen Identification Number I. Units of measurement: n/a J. Full name: age K. Definition: age of the patient L. Units of measurement: year M. Full name: gender N. Definition: 1 = Male 0 = Female O. Units of measurement: n/a 2. Parameters and/or variables used in "FPKMs.txt" Log transformed normalized FPKM data is represented, specifically a log(1+FPKM) transformation is used. FPKM is the unit of the data. FPKM = Fragments Per Kilobase of transcript per Million mapped reads. 0 is not missing data; it indicates a FPKM of 0. The gene names were from the University of California Santa Cruz human genome GRCh37/hg19, which can be found at https://genome.ucsc.edu/. Gene names are also available with the acronyms at the HUGO gene nomenclature committee website at http://www.genenames.org/cgi-bin/search?search=&submit=Submit&rows=100 SHARING/ACCESS INFORMATION 1. Licenses/restrictions placed on the data: CC BY Attribution 4.0 International 2. Links to publications that cite or use the data: Dorr C, Wu B, Guan W, Muthusamy A, Sanghavi K, Schladt DP, et al. (2015) Differentially Expressed Gene Transcripts Using RNA Sequencing from the Blood of Immunosuppressed Kidney Allograft Recipients. PLoS ONE 10(5): e0125045. doi:10.1371/journal.pone.0125045 http://dx.doi.org/10.1371/journal.pone.0125045 3. Recommended citation for the data: Dorr, Casey; Wu, Baolin; Guan, Weihua; Muthusamy, Amutha; Sanghavi, Kinjal; Schladt, David; Maltzman, Jonathan; Scherer, Steven; Brott, Marcia; Matas, Arthur; Jacobson, Pamala; Oetting, William; Israni, Ajay. (2016). Differentially Expressed Gene Transcripts Using RNA Sequencing from the Blood of Immunosuppressed Kidney Allograft Recipients [dataset]. Retrieved from the Data Repository for the University of Minnesota, http://dx.doi.org/10.13020/D6KS3R. Credits: Template provided by the University of Minnesota Libraries, http://lib.umn.edu/datamanagement