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

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.

GS-1-16：2016年9月13日，在华盛顿州文耐彻附近的一个商业果园中收获的‘Granny Smith’苹果。经过包装后，这些果实被储存在1˚C的空气中。在收获及储存后，从6个苹果的3个重复样本中收集果皮，使用蔬菜削皮器均匀地切取从果柄端至花萼端的果皮部分（结果果皮长度约为20厘米，宽度约为2厘米），并将它们置于赤道中央进行即时液氮冷冻，随后储存在-80˚C的低温环境中。这些样本代表了一个在空气储存前两周的短期时间序列采样方案（TC-0表示收获时，TC-1表示在1˚C储存1周，TC-2表示在1˚C储存2周，TE-1表示在1˚C储存1周，随后在20˚C储存5天，T1.1至T1.5代表TE-1处理期间在20˚C的24小时时间序列）。HC-1-17：‘Honeycrisp’苹果于2016年8月从华盛顿州文耐彻附近的一个商业果园获得。在空气环境中1 ˚C储存约六个月后，从单个苹果中收集果皮和皮质组织。使用直径为4毫米的活检打孔器，深度为6至8毫米，以采集组织，其中使用剃刀片立即将果皮从皮质中分离，并将两种组织分别立即用液氮冷冻，然后储存在-80 ˚C。四个样本，生物重复三次（总共12个观察值，其中每个重复样本是由10个水果的组织混合而成），分别代表具有和没有苦斑病变的苹果的果皮和皮质组织（ASP = 无症状果皮，ASC = 无症状皮质，SP = 症状性果皮，SC = 症状性皮质）。使用针对苹果组织特异性修改的CTAB/氯仿方案提取RNA（Honaas和Kahn，2017- DOI 10.1186/s13104-017-2564-2）。使用Nanodrop（ND-1000，Thermo Fisher Scientific，Waltham，MA）分析提取的RNA的量和纯度，使用Agilent Bioanalzyer 2100（G2938C，Agilent Technologies，Santa Clara，CA）及其Agilent-RNA Pico Kit（cat# 5067-1513）分析其量和完整性。仅使用符合以下标准的RNA进行下游分析：A260/A280 ≈ 2.0，RNA完整性数（RIN）≥ 8.0。