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| Status |
Public on Oct 31, 2020 |
| Title |
Vein_T2_Watered_3 |
| Sample type |
SRA |
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| Source name |
Vein Enriched Tomato Leaf section
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| Organism |
Solanum lycopersicum |
| Characteristics |
tissue: Vein
stress: watered
timepoint: T2
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| Treatment protocol |
At 25 days post sowing (DPS), timepoint 0 (T0) was collected, and 6 biological replicates of plants selected at random were subjected to drought stress by withholding water for an additional 4 days, while 6 control plants continued to receive 150 mL H2O every other day. After skipping 3 alternate day waterings (totaling 6 days since the last watering), vein and intervein tissue was captured from half of the drought-stressed plants, and half of the control plants at 29 DPS as the initial comparative drought condition, constituting Timepoint 1 (T1, i.e. T1D vs T1W, 3 plants each, 2 tissues). Drought-recovered plants were watered 150 mL H2O on 29 and 30 DPS after which both vein and intervein tissues were collected, and the same was also done for plants that constantly received water throughout the experiment (T2, i.e. T2D vs T2W, 3 plants each, 2 tissues).
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| Growth protocol |
Tomato (Solanum lycopersicum) plants were grown and subjected to drought as described in Ogden et al. 20203. Briefly, plants were grown in 4 inch pots containing 300 g soil within a Percival growth chamber under ~400 PAR light at 16/8 hours light/dark cycle. Plants were selected at random and subjected to drought stress by withholding watering for 6 days, at which point timepoint 1 (T1) samples were collected. Timepoint 2 (T2) leaves were collected 3 days after a return to normal watering. In all cases, the 4th true leaf was excised and dissected to enrich for vasculature and non-vasculature tissue (Figure 1A). Vein and inter-vein tissues were immediately flash frozen in liquid nitrogen and stored at -80° C until protein and RNA extraction.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Rneasy Plant Mini Kit, Qiagen Cat#74904, according to manufacturers instructions.
The libraries were made by the Penn State Genomics Core Facility at University Park using the Illumina TruSeq Stranded mRNA kit following the manufacturer's protocol (Illumina Inc.). Library concentration was determined by qPCR using the KAPA Library Quantification Kit Illumina platforms (KAPABiosystems) and used to make an equimolar pool of the libraries. The library pool was sequenced on two NextSeq High Output 75 nt single read sequencing runs."
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
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| Description |
Vein_T2_W_3
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| Data processing |
Quality control, FastQC v0.11.5
Alignment, HISAT2 v2.1.0
Transcript Assembly, StringTie v1.3.3b
Normalization, DESeq2 v1.20.0
Differential Expression, DESeq2 v1.20.0
Genome_build: Solanum lycopersicum (SL3.0)
Supplementary_files_format_and_content: DESeq2 normalized gene count estimate and DESeq2 differential expression matrix for VT1D vs VT1W and IVT1D vs IVT1W, file named Gene_count_matrix.xlsx
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| Submission date |
Aug 18, 2020 |
| Last update date |
Oct 31, 2020 |
| Contact name |
aaron ogden |
| E-mail(s) |
Aaronjogden@gmail.com
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| Phone |
5094328269
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| Organization name |
Pacific Northwest National Lab
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| Department |
integrative omics
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| Street address |
902 battelle boulevard
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| City |
pasco |
| State/province |
wa |
| ZIP/Postal code |
99354 |
| Country |
USA |
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| Platform ID |
GPL29032 |
| Series (1) |
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| Relations |
| BioSample |
SAMN15848078 |
| SRA |
SRX8961793 |
| 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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