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| Status |
Public on Sep 14, 2015 |
| Title |
Control 1 |
| Sample type |
SRA |
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| Source name |
control_leaves
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| Organism |
Solanum lycopersicum |
| Characteristics |
cultivar: Ailsa Craig
development stage: four-leaf stage
treatment group: mock, nightly dark environment with MgCl2 treatment
tissue: leaves
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| Treatment protocol |
Plants underwent one of four treatments: control (mock, nightly dark environment with MgCl2 treatment), RL (nightly red light treatment with MgCl2 treatment), DC3000 (nightly dark environment with DC3000 inoculation), and RL+DC3000 (nightly red light treatment with DC3000 inoculation). Leaves were collected from the plants at 5:00 AM the next day after treatment and immediately frozen in liquid nitrogen for further RNA exaction
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| Growth protocol |
Tomato (Solanum lycopersicum L, cv. Ailsa Craig) seeds were sown in trays filled with a mixture of peat and vermiculite (2:1, v/v) and placed in growth chambers at a temperature of 25/19C (day/night) with a photoperiod of 12 h of light (8:00 AM to 8:00 PM), a photosynthetic photon flux density (PPFD) of 200 umol m-2 s-1 from fluorescent tubes, and a relative humidity (RH) of 70%. The seedlings were watered daily and fertilised with Hoagland nutrition solution once per week.
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| Extracted molecule |
total RNA |
| Extraction protocol |
ReverTra Ace qRT-PCR Kit (Toyobo, Japan).
The enrichment of mRNA, fragment interruption, addition of adapters, size selection, PCR amplification, and RNA-seq were performed by staff at Zhejiang Tianke (Hangzhou, China). Poly (A) mRNA was isolated using oligo dT beads and then cleaved into short fragments. A single-end RNA-seq library was prepared for 12 samples from four different treatments, and sequenced on the Illumina HiSeq 2000 platform.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
A1
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| Data processing |
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence by fastx_toolkit-0.0.14 and masked for low-complexity or low-quality sequence.
then mapped to tomato whole genome using Bowtie 2 version 2.0.0-beta7 with parameters -S -p 15 .
Reads Per Kilobase of gene per Megabase of library size (RPKM) were calculated using cuffdiff.
The number of reads falling in the genes were counted and normalized by the size of the library.
Genome_build: SL2.31 (Annotation at: http://www.plantgdb.org/XGDB/phplib/download.php?GDB=Sl)
Supplementary_files_format_and_content: tab-delimited text file include FPKM values for each Sample,and the log2(Fold_change) normalized,_q-value,and gene annotation.
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| Submission date |
Dec 11, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Youxin Yang |
| E-mail(s) |
yangyouxinchina@163.com
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| Organization name |
Zhejiang University
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| Department |
Department of Horticulture
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| Street address |
Zijingang Campus, 866 Yuhangtang Road
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| City |
Hangzhou |
| ZIP/Postal code |
310058 |
| Country |
China |
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| Platform ID |
GPL16345 |
| Series (1) |
| GSE64087 |
RNA-seq analysis reveals the role of red light in resistance against Pseudomonas syringae pv. tomato DC3000 in tomato plants |
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| Relations |
| BioSample |
SAMN03262806 |
| SRA |
SRX806598 |
| 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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