|
| Status |
Public on Jan 01, 2020 |
| Title |
Day10_Rep2_Vrip |
| Sample type |
SRA |
| |
|
| Source name |
Vitis_riparia_Dormant_Bud
|
| Organism |
Vitis riparia |
| Characteristics |
tissue: Dormant Bud
genotype: PI588275
replicate: Rep2
|
| Treatment protocol |
Dormant canes were pruned from the vineyard. Day0 buds (3 replicate buds) were cut from the cane and plunged into liquid nitrogen. Canes were pruned to single node cuttings and placed in cups of water. Cups were placed at room temperature. Each subsequent day, replicate buds were cut from the canes and flash frozen. Five replicate collections were conducted on each collection day. Buds were collected until evidence of budburst was observed for each genotype.
|
| Growth protocol |
Two clonal vines of Vitis amurensis and Vitis riparia are maintained under standard vineyard conditions in the USDA cold hardy grapevine germplasm repository. Vitis vinifera vines are grown in a commercial vineyard under standard vineyard conditions.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from pulverized tissue using the Sigma Spectrum Plant total RNA isolation kit.
Libraries were constructed following a modified protocol based on Borodina et al 2011. Methods were modified by adding 3% w/v PVP40 to the lysis buffer to help reduce extraction inhibitors.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Barcode spltting: Fastx_Barcode_splitter.pl. Raw data files were split based on custom 6bp nucleotides
Reads were quality filtered using fastq_quality_filter (-Q33 -q 25 -p 25)
Barcodes removed from each bin using fastx_trimmer (-Q33 -f 7)
Adapter removal: cutadapt (--minimum-len 25 -O 3)
Alignment: STAR using default parameters, the 12xV2 grapevine genome and the V3 annotation file (Vitis_vinifera_gene_annotation_on_V2_v20.gff3)
Feature counting: ht-seq count (-f sam -s no -t gene)
Differential gene expression: DESeq2
Pathway Enrichment: VitisPathways
Genome_build: 12xV2 grapevine genome: https://urgi.versailles.inra.fr/Species/Vitis
Supplementary_files_format_and_content: Counts files are the output gene counts produced by htseq-count.
|
| |
|
| Submission date |
Jan 08, 2019 |
| Last update date |
Jan 02, 2020 |
| Contact name |
Alisson Kovaleski |
| E-mail(s) |
ap874@cornell.edu
|
| Organization name |
Cornell University
|
| Street address |
630 W. North Street
|
| City |
Geneva |
| State/province |
NY |
| ZIP/Postal code |
14456 |
| Country |
USA |
| |
|
| Platform ID |
GPL26020 |
| Series (1) |
| GSE124820 |
Gene regulation in wild and cultivated Vitis species during deacclimation and budbreak |
|
| Relations |
| BioSample |
SAMN10714420 |
| SRA |
SRX5227470 |
