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| Status |
Public on Apr 28, 2023 |
| Title |
VR_LD21_3 |
| Sample type |
SRA |
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| Source name |
Shoot tip
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| Organism |
Vitis riparia |
| Characteristics |
tissue: shoot tip
treatment: Long day
days of treatment: Continued LD photoperiod
genotype: V. riparia PI588259
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| Treatment protocol |
After 30 days, when grapevines reached 12-15 nodes, pots were randomized into two treatment groups. Five days after randomization, differential photoperiod treatments began with one treatment group continuing in LD and the other receiving a short photoperiod (SD, 13 h). The SD was imposed using an automated, white covered black-out system (Van Rijn Enterprises LTD, Grassie, Ontario, Canada). At 7 and 21 days of differential photoperiod treatment, four node shoot tips were collected between 8:30 and 10:30 AM, immediately frozen in liquid nitrogen, and placed at -80°C for future RNA extraction. Three replications (5 vines/replicate) were harvested.
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| Growth protocol |
Potted, spur-pruned six-year-old V. riparia ecodormant grapevines were removed from cold storage, repotted and grown under a long photoperiod (LD, 15 h) with 25/20°C + 3°C day/night temperatures and 600 to 1400 μmolm-2s-1 photosynthetic photon flux (PPF) in a climate-controlled, un-shaded glass greenhouse (En Tech Control Systems Inc., Montrose, MN) in Brookings, SD, USA (44.3°N).
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from shoot tips using the Qiagen RNeasy Midi RNA isolation kit according to manufacture protocol and as described by Mathiason et al 54, DNAased and stored at -80°C. DNA was removed by incubation with 1 unit per microgram (μg) RNase-free DNase (Promega, Madison WI) at 37°C for 30 min. RNA was purified using RNeasy plant mini columns (Qiagen, Valencia CA). RNA quality and quantity were verified with an Agilent (Santa Clara, CA) 243 Bioanalyzer RNA 6000 nano chip.
RNA seq libraries for LD and SD shoot transcriptome at 7 and 21 days were prepared and sequenced by Illumina HiScanSQ (43bp, single strand) at the Cornell University, Institute of Biotechnology Genome Facility (Ithaca, NY, USA).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiScanSQ |
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| Data processing |
Raw reads quality and adapter sequences were checked using fastqc (v. 0.11.3).
Filtered adaptor and poor quality sequences respectively, using cutadapt (v. 1.8.1) and prinseq-lite (v 0.20.4).
The reference genome based alignment and assembly of clean reads were performed using tuxedo pipeline (Trapnell et al., 2012). The Vitis vinifera reference genome (Genome12X, V1) was indexed using Bowtie2 (v.2.2.4).
Quality reads were aligned using tophat (v2.0.13) to the indexed reference genome and guided using gene model available for V. vinifera (V1.phase.gff3).
Mapped reads in each library were assembled into transcripts using cufflinks (v. 2.2.1).
Genome_build: V. vinifera reference genome (Genome12X, V1 ).
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each Sample.
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| Submission date |
Mar 06, 2017 |
| Last update date |
Apr 28, 2023 |
| Contact name |
Anne Y Fennell |
| E-mail(s) |
anne.fennell@sdstate.edu
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| Organization name |
South Dakota State University
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| Department |
Department of Plant Science
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| Lab |
Edgar S. McFadden Biostress Lab
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| Street address |
North Campus Drive
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| City |
Brookings |
| State/province |
South Dakota |
| ZIP/Postal code |
57006 |
| Country |
USA |
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| Platform ID |
GPL23121 |
| Series (1) |
| GSE95707 |
Vitis riparia shoot tip transcriptome in response to long and short photoperiod. |
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| Relations |
| BioSample |
SAMN06480765 |
| SRA |
SRX2613824 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2522401_VR_LD21_3.txt.gz |
468.4 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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