This readme.txt file was generated on 20200811 by Lu Yin ------------------- GENERAL INFORMATION ------------------- 1. Title of Dataset Trichome density phenotypic data, image data, candidate genes Nanopore sequencing data (Chapter 4 Lu Yin Ph.D. Thesis 2020) 2. Author Information Principal Investigator Contact Information Name: Matthew Clark Institution: University of Minnesota Address: 1970 Folwell Ave., Alderman 305, St. Paul, MN55108 Email: clark776@umn.edu Associate or Co-investigator Contact Information Name: Lu Yin Institution: University of Minnesota Address: 2384 Larpenteur Ave W., Apt. 10, Lauderdale, MN55113 Email: yinxx134@umn.edu 3. Date of data collection: 20181101-20200530 4. Geographic location of data collection: University of Minnesota, St. Paul campus 5. Information about funding sources that supported the collection of the data: USDA-NIFA Specialty Crop Research Initiative Award No. 2017- 51181-26829 Minnesota Department of Agriculture Specialty Crop Grant University of Minnesota grant-in-aid program -------------------------- SHARING/ACCESS INFORMATION -------------------------- 1. Licenses/restrictions placed on the data: Embargo until 2022/06/30 2. Links to publications that cite or use the data: Frontiers in Plant Science (submitted) 3. Links to other publicly accessible locations of the data: 4. Links/relationships to ancillary data sets: 5. Was data derived from another source? If yes, list source(s): 6. Recommended citation for the data: --------------------- DATA & FILE OVERVIEW --------------------- 1. File List A. Filename: LeafTrichomePhenotype.xlsx Short description: The excel file contains two experiments of phenotypic data on trichome density scores in a hybrid grape population (GE1025 family and GE1783 family). B. Filename: Folder LeafTrichomeGE1783_1env Short description: Contains GE1783 scanned images to derive trichome scores in Experiment 2. C. Filename: Folder LeafTrichomeGE1783_1envAdaVHDs Short description: Contains additional GE1783 scanned images to derive trichome scores in Experiment 2, specifically for adaxial vein simple density. D. Filename: Folder ChecksPinots Short description: Contains images to derive trichome scores parental/grandparental checks and Pinot mutants. E. Filename: Folder SequenceData Short description: Contains bam and indexed bam files for one pseudogene within our fine mapped region and three candidate genes on chromosome 1 (ZFP5, transcription factor WER, SLP21). For MN1264 and MN1246. Aligned to Pinot Noir 12X reference genome and V. riparia genome. 2. Relationship between files: Folder (B) contains images to derive trichome scores in excel file (A) sheet 2 Folder (C) contains images to derive trichome scores in excel file (A) sheet 3 Folder (D) contains images to derive trichome scores in excel file (A) sheets 4 and 5 3. Additional related data collected that was not included in the current data package: 4. Are there multiple versions of the dataset? no If yes, list versions: Name of file that was updated: i. Why was the file updated? ii. When was the file updated? Name of file that was updated: i. Why was the file updated? ii. When was the file updated? -------------------------- METHODOLOGICAL INFORMATION -------------------------- 1. Description of methods used for collection/generation of data: File (A) was obtained by viewing under a dissecting scope 22.5X (sheet 1) or zoomed-in on a computer monitor from scanned images in folder (B)-(D) (sheets 2-5). Using a 0-6 rating scale where 0 means no trichome, 6 means covered with trichomes (see publication in Frontiers in Plant Science, under review) 2. Methods for processing the data: Image folders (B)-(D) were obatined by scanning the first mature/last tender leaf using Epson Perfection V550 Photo Scanner Folder (E) was obtained by long-range PPCR, Nanopore Sequencing/shotgun sequencing as outlined by the publication 3. Instrument- or software-specific information needed to interpret the data: File (A) can be used for analysis of variance or QTL mapping as outlined in the publication Folders (B)-(D) need to be scored to derive part of file (A) Folder (E) needs Geneious to create a consensus fasta file and then visualized in SnapGene. 4. Standards and calibration information, if appropriate: 5. Environmental/experimental conditions: Regular greenhouse conditions for Experiment 1; field conditions for Experiment 2. See publication for details. 6. Describe any quality-assurance procedures performed on the data: 7. People involved with sample collection, processing, analysis and/or submission: Lu Yin Avinash Karn Lance Cadle-Davidson Cheng Zou Anna Underhill Paul Atkins Erin Treiber Daniel Voytas Matthew Clark ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: File (A) LeafTrichomePhenotype.xlsx ----------------------------------------- 1. Number of sheets: Experiment 1 (sheet 1) was conducted on greenhouse-maintained GE1025 cuttings in 2018 and 2019 and on field-grown leaves of GE1025 in 2019 (3 environments). Experiment 2 (sheets 2 and 3) was conducted on GE1783 field-grown leaves in 2019 (1 environment; sheet 3 contains additional samples on adaxial vein simple density). Sheets 4 and 5 each contains parental/grandparental checks and Pinot mutants. 2. Number of cases/rows: 456 rows 3. Missing data codes: Code/symbol Definition Code/symbol Definition ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: File (A) and folders (B)-(D) ----------------------------------------- 4. Variable List A. Name: genotype Description: genotype name GE1783-xxxx001 or xxxx001 = adaxial side GE1783-xxxx002 or xxxx002 = abaxial side