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| Status |
Public on Dec 15, 2018 |
| Title |
WD_R2 |
| Sample type |
SRA |
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| Source name |
Water Deficit_Root
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| Organism |
Vitis riparia |
| Characteristics |
water condition: Water Deficit
tissue: Root
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| Treatment protocol |
Three shoots were allowed to develop on each grapevine; after 30 days growth, when the grapevine shoots had reached 12-15 nodes, 36 grapevines were randomized into two groups: water deficit (WD) and well-watered control (C). Five days after randomization, differential water treatments began in replicates (3 vines/ replicate) of each treatment: WD received no water and C received 2 L of tap water each day. Root and shoot samples from the 14 d C and WD treatments were used for transcriptomic analysis, as this time point showed distinct physiological differences between treatments.
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| Growth protocol |
Spur-pruned, V. riparia Michx. vines were removed from cold storage, root pruned, repotted in 15 L pots, and grown under a long photoperiod (15 h) with 25/20°C ± 3°C day/night temperatures and 600 to 1400 μmol m-2 sec-1 photosynthetic photon flux 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 100 mg of each replicate (n=3) frozen pulverized shoot tips as described by Mathiason K. et al. (2009). Total RNA was extracted from root tips (5 cm) of each replicate (n=3) using the Qiagen Rneasy Midi RNA isolation kit (Qiagen, 75144) according to manufacturer protocol.
Total RNA samples were sent to Cornell University Life Sciences Core Laboratories and single-end sequences were generated using an Illumina HiSeq 2000.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
Water deficit whole root tissue
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| Data processing |
FASTQ files were explored using FASTX toolkit and cleaned using Prinseq
The cleaning procedure included, trimming low quality reads from both ends until a bp of Phred quality score >= 20 and filtering out reads having below 20 nt.
Bowtie2 V2.1.0 was used to build the index of reference genome, the 12x sequence of V. vinifera PN40024.
TopHat V2.0.8 was used to map each of the cleaned samples to the bowtie build index and Cufflinks V2.2.2 was used to quantify transcript abundance in terms of RPKM.
Differential gene expression, in WD relative to C treatments, was tested by the Cuffdiff program within Cufflinks using its default parameters. V. vinifera V1 gene annotation was used.
Genome_build: 12x V. vinifera PN40024 (http://genomes.cribi.unipd.it/DATA/)
Supplementary_files_format_and_content: text files containing count, RPKM, or cuffdiff output (as indicated in the file name) with the identifiers at:
http://plants.ensembl.org/Vitis_vinifera/Info/Index
http://www.plantgdb.org/VvGDB/
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| Submission date |
Jan 11, 2018 |
| Last update date |
Dec 15, 2018 |
| Contact name |
Anne Fennell |
| E-mail(s) |
anne.fennell@sdstate.edu
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| Phone |
605-688-6373
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| Organization name |
South Dakota State University
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| Department |
Plant Science
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| Street address |
1390 College Ave
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| City |
Brookings |
| State/province |
SD |
| ZIP/Postal code |
57007 |
| Country |
USA |
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| Platform ID |
GPL24498 |
| Series (1) |
| GSE109065 |
Shoot transcriptomic response is more sensitive to a 14 day water deficit than root transcriptomic response in Vitis riparia |
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| Relations |
| BioSample |
SAMN08348593 |
| SRA |
SRX3584207 |
| 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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