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

posted on 2024-06-11, 05:53 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.


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


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  • Non-geospatial

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  • biota

National Agricultural Library Thesaurus terms

transcriptome; gene expression

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  • Public

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It is recommended to cite the accession numbers that are assigned to data submissions, e.g. the GenBank, WGS or SRA accession numbers. If individual BioProjects need to be referenced, state that "The data have been deposited with links to BioProject accession number PRJNA475898 in the NCBI BioProject database ("

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