This readme.txt file was generated on 20200811 by Lu Yin
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GENERAL INFORMATION
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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
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SHARING/ACCESS INFORMATION
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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:
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DATA & FILE OVERVIEW
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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?
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METHODOLOGICAL INFORMATION
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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
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DATA-SPECIFIC INFORMATION FOR: File (A) LeafTrichomePhenotype.xlsx
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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
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DATA-SPECIFIC INFORMATION FOR: File (A) and folders (B)-(D)
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4. Variable List
A. Name: genotype
Description: genotype name
GE1783-xxxx001 or xxxx001 = adaxial side
GE1783-xxxx002 or xxxx002 = abaxial side