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| Status |
Public on Dec 01, 2016 |
| Title |
Oak-PV-H1 |
| Sample type |
SRA |
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| Source name |
grape berries
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| Organism |
Vitis vinifera |
| Characteristics |
cultivar: Zinfandel
vineyard: Oakville
ripening stage: Post-veraison
status: Healthy
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| Growth protocol |
Individual berries were collected from grapevines that were naturally infected with GRBaV and from healthy grapevines
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted from freeze-ground berry tissues (no seeds) using a CTAB based protocol with a chloroform denaturation step. RNA was cleaned with RNeasy kit (Qiagen, US) including the DNAse treatment on column.
Illumina TruSeq RNA Sample Prep Kit v2 protocol
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
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| Data processing |
Quality trimming of raw reads was done with Sickle v.1.210 with a threshold of 20 (Q >20).
Quality filtering was done with Scythe v.0.991 with a prior of 0.4
Bowtie2 v.2.1.0 was used to map the processed reads to the combined references with the following options: -q --end-to-end --sensitive --no-unal -p 12
Read counts were extracted from the bowtie2 alignments using the script sam2counts.py v.0.91
Genome_build: Vitis vinifera cv. PN40024 combined with NCBI accessions: YP_008400117.1, YP_008400116.1, YP_008400118.1, YP_008400114.1, YP_008400113.1, and YP_008400115.1
Supplementary_files_format_and_content: Healdsburg_grape_gene_counts.txt and Oakville_grape_genes_counts.txt: tab delimited text files, raw read counts determined by mapping trimmed sequencing reads
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| Submission date |
Aug 18, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Barbara Blanco-Ulate |
| E-mail(s) |
[email protected]
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| Organization name |
University of California, Davis
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| Department |
Plant Sciences
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| Lab |
Blanco Lab
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| Street address |
One Shields Avenue
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| City |
Davis |
| State/province |
CA |
| ZIP/Postal code |
95616 |
| Country |
USA |
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| Platform ID |
GPL22342 |
| Series (1) |
| GSE85812 |
Field systems biology of grapevine red blotch reveals the impact of viral infections on the transcriptional and hormonal regulation of berry ripening |
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| Relations |
| BioSample |
SAMN05591460 |
| SRA |
SRX2034633 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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