Data for 15N labeling of amino acids in Spirodela polyrhiza ------------------------------------------------------------------------- This repository contains data for three 15N stable isotopic labeling experiments in Spirodela polyrhiza (common duckweed). These experiments used three light and carbon input combinations: - Light grown with supplemental sucrose (mixotrophic) - Light grown without supplemental sucrose (photoautotrophic) - Dark grown with supplemental sucrose (heterotrophic) Dark with Sucrose, Light With/Without Sucrose .zip archives contains the following: --------------------------------------------------------------------------------------- - For labeling pattern folder containing: Data files from a 15N labeling time-course experiment used to model labeling pattern - For pool size folder containing: MS data files from time 0 of labeling studies grown under the same conditions used to estimate amino acid pool sizes - A README file explaining that particular experiment Modeling_Data and Pool_Size_Data .zip archives contain the following: ------------------------------------------------------------------------ - Data extracted from the .MzML files in each experimental .zip archive - Explanations and github repositories for how extracted data were obtained - README files explaining the layout of the data spreadsheets This codebook.txt file was generated on 2018-02-16 by wilsonkm ------------------- GENERAL INFORMATION ------------------- 1. Title of Dataset 15N labeling of amino acids in Spirodela Polyrhiza 2. Author Information Principal Investigator Contact Information Name: Erin M. Evans Institution: University of Minnesota Address: Email: jewet033@umn.edu Associate or Co-investigator Contact Information Name: Dana M. Freund Institution: University of Minnesota Address: Email: dfreund@umn.edu Associate or Co-investigator Contact Information Name: Veronica Sondervan Institution: University of Minnesota Address: Email: Associate or Co-investigator Contact Information Name: Jerry D. Cohen Institution: University of Minnesota Address: Email: cohen047@umn.edu Associate or Co-investigator Contact Information Name: Adrian D. Hegeman Institution: University of Minnesota Address: Email: hegm007@umn.edu 3. Date of data collection: N/A 4. Geographic location of data collection: N/A 5. Information about funding sources that supported the collection of the data: Sponsorship: National Science Foundation Plant Genome Project Grant ISO-1238812; National Science Foundation Postdoctoral Fellowship in Biology IOS-1400818 -------------------------- SHARING/ACCESS INFORMATION -------------------------- 1. Licenses/restrictions placed on the data: CC0 1.0 Universal 2. Links to publications that cite or use the data: Evans, E.M., Freund, D.M., Sondervan, V.M., Cohen, J.D., Hegeman, A.D., Metabolic patterns in Spirodela polyrhiza revealed by 15N stable isotope labeling of amino acids in photoautotrophic, heterotrophic, and mixotrophic growth conditions. (2018). Submitted to Frontiers in Chemistry 3. Links to other publicly accessible locations of the data: N/A 4. Links/relationships to ancillary data sets: N/A 5. Was data derived from another source? N/A 6. Recommended citation for the data: Evans, Erin, M; Freund, Dana, M; Sondervan, Veronica; Cohen, Jerry, D; Hegeman, Adrian, D. (2018). 15N labeling of amino acids in Spirodela Polyrhiza. Retrieved from the Data Repository for the University of Minnesota, http://hdl.handle.net/11299/193599. --------------------- DATA & FILE OVERVIEW --------------------- 1. File List A. Filename: README.txt Short description: An explanatory and over-arching README text file. B. Filename: Dark With Sucrose.zip Short description: This .zip archive folder contains two sub-folders: “For Labeling patterns” and “For Pool Sizes”. This .zip archive folder also contains a README file explaining the particular experiment. The “For labeling pattern” folder contains: Data files from a 15N labeling time-course experiment used to model labeling pattern. The “For Pool Sizes” folder contains: MS data files from time 0 of labeling studies grown under the same conditions used to estimate amino acid pool sizes. C. Filename: Light With Sucrose.zip Short description: This .zip archive folder contains two sub-folders: “For Labeling patterns” and “For Pool Sizes”. This .zip archive folder also contains a README file explaining the particular experiment. The “For labeling pattern” folder contains: Data files from a 15N labeling time-course experiment used to model labeling pattern. The “For Pool Sizes” folder contains: MS data files from time 0 of labeling studies grown under the same conditions used to estimate amino acid pool sizes. D. Filename: Light Without Sucrose.zip Short description: This .zip archive folder contains two sub-folders: “For Labeling patterns” and “For Pool Sizes”. This .zip archive folder also contains a README file explaining the particular experiment. The “For labeling pattern” folder contains: Data files from a 15N labeling time-course experiment used to model labeling pattern. The “For Pool Sizes” folder contains: MS data files from time 0 of labeling studies grown under the same conditions used to estimate amino acid pool sizes. E. Filename: Modeling_Data_Extracted.zip Short description: This .zip archive contains data extracted from the .MzMl files in each experimental .zip archive, explanations and github repositories for how extracted data were obtained, and README files explaining the layout of the data spreadsheets. F. Filename: Pool_Size_Data.zip Short description: This .zip archive contains data extracted from the .MzMl files in each experimental .zip archive, explanations and github repositories for how extracted data were obtained, and README files explaining the layout of the data spreadsheets. G. Filename: Directory.txt Short description: A plain text file of containing every .zip folder’s file directory. 2. Relationship between files: N/A 3. Additional related data collected that was not included in the current data package: N/A 4. Are there multiple versions of the dataset? N/A -------------------------- METHODOLOGICAL INFORMATION -------------------------- The authors have provided individual READMEs per each .zip file detailed below in the sections “DATA-SPECIFIC INFORMATION FOR [FILE]”. In the READMEs of the experimental .zip folders, users can find more information regarding methods, file naming conventions for .MZml files, experimental and sampling breakdown for the associated experiment including LC-MS parameters, and the content of the “For Labeling” and “For Pool Size” folders. In the READMEs of the pool size and modeling .zip folders, users can find more information regarding the contents of the .csv and/or excel spreadsheets, how to find the R scripts used for data extraction and specific instructions on how to use the input files packaged with the .MzML files, and how the models and/or pool sizes were estimated. ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: Dark With Sucrose.zip ----------------------------------------- This .zip folder contains raw data from the dark with sucrose experiment. It contains a total of 4 csv files and 55 .mzML files. In lieu of listing each .mzML file, please see Directory.txt for file directory information. The following information pertains to each .csv housed in the .zip folder. Folder: For Labeling patterns Filename: files_template.csv 1. Number of variables: 3 2. Number of cases/rows: 51 3. Missing data codes: N/A 4. Variable List A. Name: File Description: Input files for the turnover and clustering script. B. Name: Time Description: Timepoint at which samples were taken. Samples were taken at the following timepoints: 0, 1, 2, 4, 8, 16, 32, 64, and 128 hours. Additional samples were also taken at 15 and 30 min timepoints. C. Name: Set Description: Set of samples. Value labels: 1, 2, 3, 4, 5 Folder: For Labeling patterns Filename: RT_input_template.csv 1. Number of variables: 11 2. Number of cases/rows: 18 3. Missing data codes: N/A 4. Variable List A. Name: name Description: Name of the chemical compound being tracked. Letters are single-letter amino acid codes. B. Name: rt.min Description: minimum amount of retention time C. Name: rt.max Description: maximum amount of retention time D. Name: mz Description: Mass-to-charge ratio value. E. Name: number.of.labels Description: Number of labels. Values: 1, 2, 3, 4 F. Name: mz.tol Description: m/z tolerance G. Name: labels Description: Type of isotopic label used. H. Name: l1.mz Description: Exact mass of the single labeled compound. I. Name: l2.mz Description: Exact mass of the double labeled compound. J. Name: l3.mz Description: Exact mass of the triple labeled compound. K. Name: l4.mz Description: Exact mass of the quadruple labeled compound. Folder: For Pool Sizes Filename: Ghostweed_Quantification_Input.csv 1. Number of variables: 8 2. Number of cases/rows: 20 3. Missing data codes: N/A 4. Variable List A. Name: name Description: Name of the chemical compound being tracked. Letters are single-letter amino acid codes. B. Name: rt.min Description: minimum amount of retention time C. Name: rt.max Description: maximum amount of retention time D. Name: mz Description: Mass-to-charge ratio value. E. Name: number.of.labels Description: Number of labels. F. Name: mz.tol Description: m/z tolerance G. Name: labels Description: Type of isotopic label used. H. Name: l1.mz Description: Exact mass of the single labeled compound. Folder: For Pool Sizes Filename: quantification_template.csv 1. Number of variables: 3 2. Number of cases/rows: 6 3. Missing data codes: N/A 4. Variable List A. Name: File Description: Input files used to exploit the turnover algorithm to generate a ratio used to estimate pool size. B. Name: Time Description: Timepoint at which samples were taken. C. Name: Set Description: Set of sample. Value labels: 1, 2, 3, 4, 5 ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: Light With Sucrose.zip ----------------------------------------- This .zip folder contains raw data from the light with sucrose experiment. It contains a total of 4 csv files and 50 .mzML files. In lieu of listing each .mzML file, please see Directory.txt for file directory information. The following information pertains to each .csv housed in the .zip folder. Folder: For Labeling patterns Filename: files_template.csv 1. Number of variables: 3 2. Number of cases/rows: 41 3. Missing data codes: N/A 4. Variable List A. Name: File Description: Files used to generate the models based on the decay of the unlabled isotopomer B. Name: Time Description: Timepoint at which samples were taken. Samples were taken at the following timepoints: 0, 1, 2, 4, 8, 16, 32, 64, and 128 hours. Additional samples were also taken at 15 and 30 min timepoints. C. Name: Set Description: Set of sample. Value labels: 1, 2, 3, 4, 5 Folder: For Labeling patterns Filename: RT_input_template.csv 1. Number of variables: 11 2. Number of cases/rows: 19 3. Missing data codes: N/A 4. Variable List A. Name: name Description: Name of the chemical compound being tracked. Letters are single-letter amino acid codes. B. Name: rt.min Description: minimum amount of retention time C. Name: rt.max Description: maximum amount of retention time D. Name: mz Description: Mass-to-charge ratio value. E. Name: number.of.labels Description: Number of labels. Values: 1, 2, 3, 4 F. Name: mz.tol Description: m/z tolerance G. Name: labels Description: Type of isotopic label used. H. Name: l1.mz Description: Exact mass of the single labeled compound. I. Name: l2.mz Description: Exact mass of the double labeled compound. J. Name: l3.mz Description: Exact mass of the triple labeled compound. K. Name: l4.mz Description: Exact mass of the quadruple labeled compound. Folder: For Quantification Filename: Quantification_Input_template.csv 1. Number of variables: 8 2. Number of cases/rows: 20 3. Missing data codes: N/A 4. Variable List A. Name: name Description: Name of the chemical compound being tracked. Letters are single-letter amino acid codes. B. Name: rt.min Description: minimum amount of retention time C. Name: rt.max Description: maximum amount of retention time D. Name: mz Description: Mass-to-charge ratio value. E. Name: number.of.labels Description: Number of labels. F. Name: mz.tol Description: m/z tolerance G. Name: label Description: Type of isotopic label used. H. Name: l1.mz Description: Exact mass of the single labeled compound. Folder: For Quantification Filename: RTinput_template.csv 1. Number of variables: 11 2. Number of cases/rows: 19 3. Missing data codes: N/A 4. Variable List A. Name: name Description: Name of the chemical compound being tracked. Letters are single-letter amino acid codes. B. Name: rt.min Description: minimum amount of retention time C. Name: rt.max Description: maxiumum amount of retention time D. Name: mz Description: Mass-to-charge ratio value. E. Name: number.of.labels Description: Number of labels. Values: 1, 2, 3, 4 F. Name: mz.tol Description: m/z tolerance G. Name: labels Description: Type of isotopic label used. H. Name: l1.mz Description: Exact mass of the single labeled compound. I. Name: l2.mz Description: Exact mass of the double labeled compound. J. Name: l3.mz Description: Exact mass of the triple labeled compound. K. Name: l4.mz Description: Exact mass of the quadruple labeled compound. ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: Light Without Sucrose.zip ----------------------------------------- This .zip folder contains raw data from the light without sucrose experiment. It contains a total of 4 csv files and 50 .mzML files. In lieu of listing each .mzML file, please see Directory.txt for file directory information. The following information pertains to each .csv housed in the .zip folder. Folder: For Labeling patterns Filename: files_template.csv 1. Number of variables: 3 2. Number of cases/rows: 31 3. Missing data codes: N/A 4. Variable List A. Name: File Description: File name. B. Name: Time Description: Timepoint at which samples were taken. Samples were taken at the following timepoints: 0, 1, 2, 4, 8, 16, 32, 64, and 128 hours. Additional samples were also taken at 15 and 30 min timepoints. C. Name: Set Description: Set of sample Value labels: 1, 2, 3 Folder: For Labeling patterns Filename: RT_input_template.csv 1. Number of variables: 11 2. Number of cases/rows: 18 3. Missing data codes: 4. Variable List A. Name: name Description: Name of the chemical compound being tracked. Letters are single-letter amino acid codes. B. Name: rt.min Description: minimum amount of retention time C. Name: rt.max Description: maximum amount of retention time D. Name: mz Description: Mass-to-charge ratio value. E. Name: number.of.labels Description: Number of labels. Values: 1, 2, 3, 4 F. Name: mz.tol Description: m/z tolerance G. Name: labels Description: Type of isotopic label used. H. Name: l1.mz Description: Exact mass of the single labeled compound. I. Name: l2.mz Description: Exact mass of the double labeled compound. J. Name: l3.mz Description: Exact mass of the triple labeled compound. K. Name: l4.mz Description: Exact mass of the quadruple labeled compound. Folder: For Pool Sizes Filename: files_quanitification.csv 1. Number of variables: 3 2. Number of cases/rows: 6 3. Missing data codes: N/A 4. Variable List A. Name: File Description: Corresponding file. B. Name: Time Description: Timepoint at which samples were taken. C. Name: Set Description: Replicate is the biological replicate for that experiment. Each experiment had 3-5 biological replicates. Folder: For Pool Sizes Filename: Quantification_input_template.csv 1. Number of variables: 8 2. Number of cases/rows: 20 3. Missing data codes: N/A 4. Variable List A. Name: name Description: Name of the chemical compound being tracked. Letters are single-letter amino acid codes. B. Name: rt.min Description: minimum amount of retention time C. Name: rt.max Description: maximum amount of retention time D. Name: mz Description: Mass-to-charge ratio value. E. Name: number.of.labels Description: Number of labels. Values: 1, 2, 3, 4 F. Name: mz.tol Description: m/z tolerance G. Name: label Description: Type of isotopic label used. H. Name: l1.mz Description: Exact mass of the single labeled compound. ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: Modeling_Data_Extracted.zip ----------------------------------------- Filename: All_Data_N0.csv This contains extracted data from the clustering algorithm for the unlabeled isotopomer. More in-depth information, including information about the clustering algorithm, can be found in the README.txt in the Modeling_Data_Extracted.zip. 1. Number of variables: 8 2. Number of cases/rows: 2115 3. Missing data codes: N/A 4. Variable List A. Name: Amino Acid Description: Name of amino acid. B. Name: Time Description: Timepoint at which samples were taken. Samples were taken at the following timepoints: 0, 1, 2, 4, 8, 16, 32, 64, and 128 hours. Additional samples were also taken at 15 and 30 min timepoints. C. Name: Replicate Description: Replicate is the biological replicate for that experiment. Each experiment had 3-5 biological replicates. D. Name: Ratio Description: Abundance ratio E. Name: Isotopomer Description: Isotopomer name. F. Name: Experiment Description: Datapoint’s associated experiment: Dark with Sucrose, Light with Sucrose, Light without Sucrose. G. Name: Cluster Description: Cluster number Value labels: 1, 2, 3, 4 H. Name: Nitrogens Description: One, multi Filename: Model_Setup_Experiments.R This file contains the parameters used to generate an exponential decay model for each individual amino acid. The model parameters k and c are referenced in the pool size data folder.