This codebook.txt file was generated on 2018-01-19 by wilsonkm ------------------- GENERAL INFORMATION ------------------- 1. Title of Dataset A consistent and predictable commercial broiler chicken bacterial microbiome in antibiotic-free production displays strong correlations with performance 2. Author Information Principal Investigator Contact Information Name: Timothy J Johnson Institution: University of Minnesota Address: Saint Paul, MN Email: tjj@umn.edu Associate or Co-investigator Contact Information Name: Bonnie P Youmans Institution: University of Minnesota Address: Saint Paul, MN Email: byoumans@umn.edu Associate or Co-investigator Contact Information Name: Sally Noll Institution: University of Minnesota Address: Saint Paul, MN Email: nollx001@umn.edu Associate or Co-investigator Contact Information Name: Carol Cardona Institution: University of Minnesota Address: Saint Paul, MN Email: ccardona@umn.edu Associate or Co-investigator Contact Information Name: Nicholas Evans Institution: PMI Nutritional Additives Address: Shoreview, MN Email: evans436@umn.edu Associate or Co-investigator Contact Information Name: Peter Karnezos Institution: PMI Nutritional Additives Address: Shoreview, MN Email: TPKarnezos@landolakes.com Associate or Co-investigator Contact Information Name: John Ngujiri Institution: The Ohio State University Address: Wooster, OH Email: ngunjiri.1@osu.edu Associate or Co-investigator Contact Information Name: Michael Abundo Institution: The Ohio State University Address: Wooster, OH Email: abundo.1@osu.edu Associate or Co-investigator Contact Information Name: Chang-Won Lee Institution: The Ohio State University Address: Wooster, OH Email: lee.2854@osu.edu 3. Date of data: 2016-03-01 - 2016-11-30 4. Geographic location of data collection: Minnesota, USA 5. Information about funding sources that supported the collection of the data: Sponsorship: USDA-AFRI Grant nos. 2016-67015-24911 and 2015-68004-23131 -------------------------- SHARING/ACCESS INFORMATION -------------------------- 1. Licenses/restrictions placed on the data: CC0 1.0 Universal 2. Links to publications that cite or use the data: N/A 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: Johnson, Timothy J; Youmans, Bonnie P; Noll, Sally; Cardona, Carol; Evans, Nicholas; Kernezos, Peter; Ngunjiri, John; Abundo, Michael; Lee, Chang-Won. (2018). A consistent and predictable commercial broiler chicken bacterial microbiome in antibiotic-free production displays strong correlations with performance. Retrieved from the Data Repository for the University of Minnesota, http://hdl.handle.net/11299/192762. --------------------- DATA & FILE OVERVIEW --------------------- Please note: This dataset contains over 4,000 files total. Files A-M, listed below, are tape archive folders that contain hundreds of .fastq.gz files in each folder. The filenames do not necessarily have meaning. GNP was the location where the work was performed. The number following GNP is a random unique number assigned to each sample. Everything following that (S#, L001, R#, 001, etc.) are sequencing designations by a sequencing facility. The only thing that has meaning is the number following GNP, which corresponds to the metadata file sample prefix column. A. Filename: chunk1.tar Short description: Contains 417 .fastq.gz files. B. Filename: chunk2.tar Short description: Contains 341 .fastq.gz files. C. Filename: chunk3.tar Short description: Contains 335 .fastq.gz files. D. Filename: chunk4.tar Short description: Contains 319 .fastq.gz files. E. Filename: chunk5.tar Short description: Contains 393 .fastq.gz files. F. Filename: chunk6.tar Short description: Contains 453 .fastq.gz files. G. Filename: chunk7.tar Short description: Contains 399 .fastq.gz files. H. Filename: chunk8.tar Short description: Contains 379 .fastq.gz files. I. Filename: chunk9.tar Short description: Contains 283 .fastq.gz files. J. Filename: chunk10.tar Short description: Contains 279 .fastq.gz files. K. Filename: chunk11.tar Short description: Contains 307 .fastq.gz files. L. Filename: chunk12.tar Short description: Contains 395 .fastq.gz files. M. Filename: chunk13.tar Short description: Contains 299 .fastq.gz files. N. Filename: chunk14.tar Short description: Contains 110 .fastq.gz files. "H20" contained within this file indicates water blank controls for sequencing, whereas "BLANK" without "H2O" indicates negative DNA extraction controls. O. Filename: Sample_metasheet_for_DRUM.xlsx Short description: Contains metadata pertaining to samples. The sheet contains a list of the samples, organism, host, isolation source, collection date, geographic location, age of bird, flock number (1-4), flock cycle (1, 2, 5), sample type, and corresponding .tar file. It does not contain metadata pertaining to chunk14.tar, which contains negative controls for the study. 2. Relationship between files: Sample_metasheet_for_DRUM.xlsx contains metadata pertaining to chunk#.tar files. 3. Additional related data collected that was not included in the current data package: N/A 4. Are there multiple versions of the dataset? No -------------------------- METHODOLOGICAL INFORMATION -------------------------- 1. Description of methods used for collection/generation of data: 2. Methods for processing the data: These are raw data directly from Illumina MiSeq after demultiplexing. 3. Instrument- or software-specific information needed to interpret the data: Illumina MiSeq 2x300 PE 4. Standards and calibration information, if appropriate: Negative controls included water blanks and extraction controls, also a mock data control 5. Environmental/experimental conditions: 6. Describe any quality-assurance procedures performed on the data: 7. People involved with sample collection, processing, analysis and/or submission: ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: Sample_metasheet_for_DRUM ----------------------------------------- 1. Number of variables: 12 2. Number of cases/rows: 2,310 rows 3. Missing data codes: N/A 4. Variable List A. Name: Sample prefix Description: Sample prefix accompanying corresponding file. B. Name: Organism Description: The most descriptive organism name for this sample (to the species, if relevant). C. Name: host Description: The natural (as opposed to laboratory) host to the organism from which the sample was obtained. Use the full taxonomic name, eg, "Homo sapiens". D. Name: isolation_source Description: Describes the physical, environmental and/or local geographical source of the biological sample from which the sample was derived. E. Name: collection_date Description: Date of sampling, in "DD-Mmm-YYYY", "Mmm-YYYY" or "YYYY" format (eg., 30-Oct-1990, Oct-1990 or 1990) or ISO 8601 standard "YYYY-mm-dd", "YYYY-mm" or "YYYY-mm-ddThh:mm:ss" (eg., 1990-10-30, 1990-10 or 1990-10-30T14:41:36) F. Name: geo_loc_name Description: Geographical origin of the sample; use the appropriate name from this list http://www.insdc.org/documents/country-qualifier-vocabulary. Use a colon to separate the country or ocean from more detailed information about the location, eg "Canada: Vancouver" or "Germany: halfway down Zugspitze, Alps" G. Name: lat_lon Description: The geographical coordinates of the location where the sample was collected. Specify as degrees latitude and longitude in format "d[d.dddd] N|S d[dd.dddd] W|E", eg, 38.98 N 77.11 W H. Name: Age of Bird Description: Age of bird by day at time of euthanasia. Value labels: D0 D07 D14 = Day 14 D21 = Day 21 D28 = Day 28 D28 = Day 35 D42 = Day 42 I. Name: Flock number Description: Number of flock. Value labels: 1 2 3 4 J. Name: Flock cycle Description: Flock cycle. Alphanumerical figure or month. Value labels: C2 C5 C1 Feb Jan Mar K. Name: Sample type Description: Type of sample. Value labels: cecum, ileum, trachea L. Name: Tar File Description: This column denotes which tar file (Chunk1, Chunk2, etc.) columns A-E correspond.