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| Status |
Public on Jan 09, 2020 |
| Title |
Cf_24h_1 |
| Sample type |
SRA |
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| Source name |
leaf tissue
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| Organism |
Solanum lycopersicum |
| Characteristics |
cultivar: VF36
age: 4.5 week-old
elicitor: Cladosporium fulvum
time point (hour post inoculation): 24h
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| Treatment protocol |
Leaflets of tomato VF36 plants were hand-inoculated using a needleless 1 mL syringe with: 1) fungal elicitors: chitin (0.5 mg/mL in water), M. restricta(OD600= 0.5 in water) or C. fulvum(OD600= 1.0 in water); 2) bacterial elicitors: flg22 (1 μM in water), S. epidermidis(OD600= 1.0 in water), P. acnes(OD600= 1.0 in water) or X. euvesicatoria(OD600= 0.2 in 10mM MgCl2); or 3) mock (water, control) (FigureS1). After treatment, leaves (one leaf from three individual plants per treatment, n=3) were collected at 12, 24, and 48 hours post-inoculation (hpi) using a razor, flash frozen by liquid nitrogen, and stored at -80°C for gene profiling and RNA-Sequencing (RNA-Seq).
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| Growth protocol |
Tomato (Solanum lycopersicum) plant cultivar VF36 was grown in a greenhouse (16h light, 25-28°C). For experiments, 4.5 week-old tomato was used.
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| Extracted molecule |
total RNA |
| Extraction protocol |
cDNA library was prepared from RNA isolated from the elicited tomato leaves (two biological replicates for each treatment per time point, 54 samples total) using the NEBNext mRNA Library Prep Master Mix Set for Illumina.
A multiplexed RNA-Seq cDNA library was PCR amplified using NEBNext Multiplex Oligos for Illumina according to the manufacturer’s instructions (New England Biolabs). The quality and average length (insert size was approximately 200 bp) of cDNAs in the library were determined using a High Sensitivity DNA chip on a 2100 Bioanalyzer (Agilent Technologies).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
The FASTX-toolkit was used for quality assessment and cleaning of reads
The reference fasta files (SL2.50) were pre-processed into an index using Bowtie 2
Quality reads were aligned to the Heinz tomato genome using TopHat 2
Aligned sequence pairs were counted with HTSeq
Reads counts were analyzed using edgeR to identify differentially expressed genes between treatments, resulting in counts per million (CPM) mapped reads
Genome_build: SL2.50
Supplementary_files_format_and_content: counts files include CPM values for each Sample
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| Submission date |
Dec 10, 2018 |
| Last update date |
Jan 10, 2020 |
| Contact name |
Elizabeth Sattely |
| E-mail(s) |
sattely@stanford.edu
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| Organization name |
Stanford University
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| Department |
Shriram Center for Biological and Chemical Engineering
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| Lab |
Room 271
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| Street address |
443 Via Ortega
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| City |
Stanford |
| State/province |
California |
| ZIP/Postal code |
94305 |
| Country |
USA |
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| Platform ID |
GPL16345 |
| Series (1) |
| GSE123543 |
A pathogen-responsive gene cluster for the production of highly modified fatty acids in tomato |
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| Relations |
| BioSample |
SAMN10564324 |
| SRA |
SRX5123291 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3506397_Cf_24h_1.count.txt.gz |
141.9 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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