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| Status |
Public on Apr 08, 2020 |
| Title |
BI16_67 |
| Sample type |
SRA |
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| Source name |
nor_MG-like_Wounded
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| Organism |
Solanum lycopersicum |
| Characteristics |
genotype: nor
ripening stage: MG-like
treatment: Wounded
tissue: fruit pericarp and epidermal tissue of the blossom end halves
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| Extracted molecule |
total RNA |
| Extraction protocol |
At 1 dpi, fruit pericarp and epidermal tissue of the blossom end halves of healthy, wounded, and infected fruit were collected and immediately frozen in liquid nitrogen. Frozen tissue was lysed using a Retsch® Mixer Mill MM 400. A total of 1 gram of ground material was used during for RNA extraction as described in Blanco-Ulate et al., 2013. Purity and concentration of the extracted RNA were determined with the use of the NanoDrop One Spectrophotometer (Thermo Scientific), followed by a more precise concentration measurement with the Qubit 3 (Invitrogen). The integrity of the RNA was confirmed via agarose gel electrophoresis.
cDNA libraries were prepared using the Illumina TruSeq RNA Sample Preparation Kit v.2 (Illumina, CA) from isolated RNA. Each library was barcoded and analyzed with the High Sensitivity DNA Analysis Kit for the Agilent 2100 Bioanalyzer (Agilent Technologies, CA). Libraries were sequenced as single-end 50-bp reads on an Illumina HiSeq 4000 platform by the DNA Technologies Core at the UC Davis Genome Center.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
2016BI67
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| Data processing |
Quality and adapter trimming was done with Trimmomatic 0.33 with the parameters ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Bowtie2 2.3.4 was used to map the reads to a combined transcriptome of tomato and the pathogen of interest with the following settings: --end-to-end --sensitive --no-unal -q -t -p 20
Read counts were extracted form the bowtie2 alignments using the script sam2counts.py v.0.91
Genome_build: Solanum lycopersicum SL4.0, B. cinerea ASM83294v1, F. acuminatum GGXD00000000, R. stolonifer GGWM00000000
Supplementary_files_format_and_content: Read_counts.csv; comma-delimited file determined by mapping trimmed sequencing reads
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| Submission date |
Apr 07, 2020 |
| Last update date |
Apr 09, 2020 |
| Contact name |
Barbara Blanco-Ulate |
| E-mail(s) |
bblanco@ucdavis.edu
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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 |
GPL25655 |
| Series (1) |
| GSE148217 |
Tomato fruit susceptibility to fungal disease is not an inevitable outcome of ripening and can be uncoupled by targeting susceptibility factors |
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| Relations |
| BioSample |
SAMN14548806 |
| SRA |
SRX8073270 |
| 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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