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Malus domestica cultivar:Granny Smith and Honey crsip Transcriptome or Gene expression

dataset
posted on 2024-01-26, 23:22 authored by Claude dePamphilis Lab, Penn State University, United States Dept of Agriculture, Agricultural Research Service, Loren Honaas
GS-1-16: ‘Granny Smith’ apples were obtained the day of harvest, 13 September, 2016, from a commercial orchard near Wenatchee, WA USA. Boxed fruit was then stored at 1˚C in air. Fruit peel was collected at harvest and after storage from 3 replicates of 6 apples each using a vegetable peeler. Evenly spaced peel sections (n=3 for each fruit) cut from the stem end to calyx end (resultant peels were ~20 cm x 2 cm) and centered at the equator were immediately flash frozen on liquid nitrogen and stored at -80˚C. These samples represent a short time course sampling scheme in the first two weeks of air storage (TC-0 = at harvest, TC-1 = 1 week at 1˚C, TC-2 = 2 weeks at 1˚C, TE-1 = 1 week at 1˚C, then 5 days at 20˚C, T1.1 through T1.5 are a 24 hour time course of the 5 days at 20˚C TE-1 treatment).HC-1-17: ‘Honeycrisp’ apples were obtained in August 2016 from a commercial orchard near Wenatchee, WA USA. Fruit peel and cortical tissue were collected from individual apples after approximately six months of boxed storage at 1 ˚C in air. A 4-mm biopsy punch, to depth of 6 to 8 mm, was used to harvest tissues, where the peel was immediately separated from the cortex using a razor blade and both tissues immediately frozen separately in liquid nitrogen, then stored at -80 ˚C. Four samples, in biological triplicate (a total of 12 observations - where each replicate was a pool of tissues from 10 fruit), represent peel and cortical tissues each from fruit with and without bitter pit lesions (ASP = asymptomatic peel, ASC = asymptomatic cortex, SP = symptomatic peel, SC = symptomatic cortex).RNA was extracted using a CTAB/Chloroform protocol modified specifically for pome fruit tissue (Honaas and Kahn, 2017- DOI 10.1186/s13104-017-2564-2). Extracted RNA was analyzed for quantity and purity using the Nanodrop (ND-1000, Thermo Fisher Scientific, Waltham, MA) and for quantity and integrity on the Agilent Bioanalzyer 2100 (G2938C, Agilent Technologies, Santa Clara, CA) with the Agilent-RNA Pico Kit (cat# 5067-1513). Only RNA that met the following standards was used for downstream analysis: A260/A280  2.0, RNA Integrity Number (RIN) of ≥ 8.0.

Funding

Agricultural Research Service, 2094-43000-007-00-D

History

Data contact name

BioProject Curation Staff

Publisher

National Center for Biotechnology Information

Temporal Extent Start Date

2018-06-13

Theme

  • Non-geospatial

ISO Topic Category

  • biota

National Agricultural Library Thesaurus terms

transcriptome; gene expression

Pending citation

  • No

Public Access Level

  • Public

Accession Number

PRJNA475898

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