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Sample GSM5578118

Query DataSets for GSM5578118

Status

Public on Jan 25, 2022

Title

Sample 53_Acclimation_Control_4_4

Sample type

SRA

Source name

leaf_Control_4h-post-treatment_Acclimation

Organism

Vitis vinifera

Characteristics

genotype: Cabernet Franc
treatment: Control
time: 4h-post-treatment
experiment: Acclimation
tissue: leaf
replicate: 4
molecule subtype: 3' mRNA

Treatment protocol

The acclimation experiment involved two treatments (control and ABA) in quadruplicates using randomized complete block design. For control treatment, the solution was composed of deionized water with 0.05% (v/v) Tween-20 (Acros Organic, Hampton, NH, USA) as surfactant. For ABA treatment, the solution was composed of 500 mg· L-1 (1.9 mM) S-ABA diluted from ProTone® SG (Valent BioSciences Corporation, Libertyville, IL, USA) and 0.05 % (v/v) Tween-20 as surfactant. Treatments were applied at noon of 18 Aug 2018 when the leaf age of base node was 95 days. Both treatments were sprayed on all grapevine leaves until runoff to ensure a full coverage. In the deacclimation experiment, cuttings were randomized and divided into six groups, corresponding to six timepoints for post treatment sample collection. When single bud cuttings developed to ‘woolly buds’ stage, treatments were applied on each group with a hand sprayer to runoff. Control treatment was deionized water, and ABA treatment was 1322 mg· L-1 (5mM) S-ABA diluted from ProTone® SG (Valent BioSciences Corporation, Libertyville, IL, USA).

Growth protocol

In the acclimation experiment, two-year-old, self-rooted ‘Cabernet Franc’ grapevines were potted-grown in greenhouse the Ohio Agricultural Research and Development Center (OARDC, Wooster, OH, USA). In the greenhouse, temperature was set at 22 °C/19 °C (day/night), lighting was maintained at 500 μmol m−2∙s-1 for a 10 h minimum photoperiod and shade was used to avoid overheating in the greenhouse. In the deacclimation experiment, dormant canes were harvested from from field-grown ‘Cabernet Franc’ grapevines in March of 2017, after vines had been exposed to >1200 chilling hours (NC model), and chopped into single node cuttings. Cuttings were incubated with cut ends in cups of water under permissive growing conditions (22 °C and 16/8 h light/dark) in a growth room.

Extracted molecule

total RNA

Extraction protocol

Total RNA was extracted using SpectrumTM Plant Total RNA Kit (Sigma Aldrich, St Louis, MO, USA) following the protocol suggested by the manufacturer
Libraries were constructed with Lexogen QuantSeq 3’mRNA-Seq Prep Kit (Lexogen, Greenland, NH, USA) following standard practices as a service provided by Cornell University Institute of Genomic Diversity (Ithaca, NY, USA). Sequencing of the libraries was accomplished using NextSeq500 (Illumina, Inc., San Diego, CA, USA) with 95 samples per lane at Cornell University Institute of Biotechnology (Ithaca, NY, USA). The read length was 85 bp and 75 bp in the acclimation and deacclimation experiment, respectively. For each library, sequencing was conducted in triplicate to justify technical validity.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina NextSeq 500

Description

11769_5751_120099_H22JMBGXG_NSF021_C07_ABA_2018_C_4_3_1_CACTAA_R1

Data processing

FastQC for quality control
BBDuk for removing adaptors and poly-A following the pipeline suggested by the manufacturer (https://www.lexogen.com/quantseq-data-analysis/)
STAR for gene level quantification using ‘-quantMode GeneCounts’
Low count gene filterig based on 'total gene count greater than sample number'
DESeq2 for variance stabilization transformation and gene expression normalization
WGCNA for gene co-expression analysis, noise gene filtering, module eigengene visualization and contrast generation
GSEA for pathway enrichment analysis
Genome_build: Vitis vinifera 12X.v2 genome with VCost.v3 annotation
Supplementary_files_format_and_content: Two matrix tables with raw gene counts for every gene and every sample without any filtering

Submission date

Sep 14, 2021

Last update date

Jan 25, 2022

Contact name

Hongrui Wang

E-mail(s)

hw692@cornell.edu

Phone

6072623547

Organization name

Cornell University