 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Apr 28, 2021 |
| Title |
VR_SD1 |
| Sample type |
SRA |
| |
|
| Source name |
BUD, short day
|
| Organism |
Vitis riparia |
| Characteristics |
days of treatment: 28 day of Short Day photoperiod
genotype: V. riparia PI588259
tissue: bud
|
| Treatment protocol |
Ten vine experimental units were randomly assigned either to continued LD or short photoperiod (SD, 13h) as previously described (Fennell et al., 2015). After 28 days, three replicate bud samples for each photoperiod were harvested into separate tubes of liquid nitrogen and stored at -80C until small RNA or total RNA extraction.
|
| Growth protocol |
Spur pruned ecodormant V. riparia vines 6-year-old were repotted and grown in long photoperiod (LD, 15h) at 25/20 ± 3°C day/night temperatures with 600–1400 mol m−2 s−1 photosynthetic photon flux in a climate-controlled unshaded glass greenhouse (En Tech Control Systems Inc., Montrose, Minn.) in Brookings, South Dakota (44.3 N). Grapevines were grown for 30 days post bud break reaching shoot lengths of 10-15 nodes.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from each replicate of LD and SD buds using a modified method of (Sreekantan et al., 2010; Fennell et al., 2015). DNA free RNA quality and quantity were verified with an Agilent (Santa Clara, CA) 2100 Bioanalyzer RNA 6000 nano chip.
RNA seq libraries for LD and SD buds transcriptome were prepared and sequenced by Illumina HiScanSQ (100 bp, single strand) at the Cornell University Institute of Biotechnology Genome Facility (Ithaca, NY, USA).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiScanSQ |
| |
|
| 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) (Schmieder & Edwards, 2011)
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.
|
| |
|
| Submission date |
Feb 27, 2017 |
| Last update date |
Apr 28, 2021 |
| Contact name |
Anne Y Fennell |
| E-mail(s) |
anne.fennell@sdstate.edu
|
| Organization name |
South Dakota State University
|
| Department |
Department of Plant Science
|
| Lab |
Edgar S. McFadden Biostress Lab
|
| Street address |
North Campus Drive
|
| City |
Brookings |
| State/province |
South Dakota |
| ZIP/Postal code |
57006 |
| Country |
USA |
| |
|
| Platform ID |
GPL23121 |
| Series (1) |
| GSE95429 |
Vitis riparia bud transcriptome in response to long and short photoperiod. |
|
| Relations |
| SRA |
SRX2595042 |
| BioSample |
SAMN06472419 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2510613_VR_SD1.txt.gz |
469.2 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
