|
| Status |
Public on Mar 31, 2023 |
| Title |
f2_040_28S2 |
| Sample type |
SRA |
| |
|
| Source name |
F2 040 short day at 28 days
|
| Organism |
Vitis |
| Characteristics |
genotype: F2 040
photoperiod: Short
|
| Treatment protocol |
Spur-pruned F2 040 and 110 grapevines were grown under long days until shoots reached 12-15 nodes, vines were randomized into LD (15 h) or SD (13 h) treatment, grown for an additional 28 or 42 days prior to bud harvest.
|
| Growth protocol |
F2 040 and F2 110 genotypes were previously described as part of a larger F2 population (Fennell et al., 2005, Acta Hort 689:533-539). Spur-pruned grapevines were grown under long days until shoots reached 12-15 nodes and then randomized into a continued long (LD, 15 h) or short photoperiod (13 h) for 28 or 42 days (George et al. 2018, J.Prot:187:13-24)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted at 28 and 42 days of long day and short day photoperiod.
Single end RNAseq libraries were prepared with TruSeq Stranded RNA Sample Prep Kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Fastq files were generated and multiplexed with bcl2fastq.
Quality of raw sequence reads were checked using FastQC.
Sequence reads were trimmed for adapters, length of 20 nucleotides, quality of 20 nucleotides using cutadapt and prinseq respectively.
Cleaned sequence reads were aligned to the Vitis vinifera 12X.V1 genome using Tophat and Gene expression levels in FPKM were quantified using Cufflinks.
Differential gene expression analysis was performed using EdgeR
Genome_build: 12X.V1
Supplementary_files_format_and_content: Tab-delimited text files
|
| |
|
| Submission date |
Mar 28, 2019 |
| Last update date |
Mar 31, 2023 |
| Contact name |
Anne Fennell |
| E-mail(s) |
anne.fennell@sdstate.edu
|
| Phone |
605-688-6373
|
| Organization name |
South Dakota State University
|
| Department |
Plant Science
|
| Street address |
1390 College Ave
|
| City |
Brookings |
| State/province |
SD |
| ZIP/Postal code |
57007 |
| Country |
USA |
| |
|
| Platform ID |
GPL26359 |
| Series (1) |
| GSE128966 |
Transcriptomic analysis of photoperiod regulated dormancy induction in grapevine. |
|
| Relations |
| BioSample |
SAMN11269657 |
| SRA |
SRX5586454 |
