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| Status |
Public on Dec 01, 2018 |
| Title |
FC17-25 |
| Sample type |
SRA |
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| Source name |
Inoculated fruit
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| Organism |
Solanum lycopersicum |
| Characteristics |
ripening stage: MG
days post inoculation: 3
agent: Rhizopus stolonifer
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| Extracted molecule |
total RNA |
| Extraction protocol |
Two grams of tissue per sample were ground in liquid nitrogen and 10mL of the RNA extraction buffer (CTAB 2% v/v, PVP 2%v/v, 100mMTris pH 8, 2MNaCl, 25mM EDTA, 0.5 g/L spermidine, 10mM β-mercaptoethanol) were added. The samples were immediately incubated for 5min at 65◦C. Two extractions with one equal volume of chloro- form:isoamyl alchohol (24:1, v/v) followed by centrifugation at 4000 rpm for 45 min at 4◦C were performed. The supernatant was recovered and 1/10 volume of 1MKOAc was added followed by centrifugation at 4000 rpm for 20 min at 4◦C. The super- natant was collected and 1/4 volume of 10M LiCl was added. Samples were incubated overnight at−20◦C and then centrifuged at 4000 rpm for 45 min at 4◦C. The supernatant was discarded and the RNA pellet was further purified using the RNeasy Plant Mini Kit (Qiagen®). DNAse treatment (RNase-Free DNase Set,Qiagen®) was done in column during the purification step. The RNA was resuspended in 35µL of nuclease-free water. The RNA concentration and purity were measured using NanoDrop 2000c Spectrophotometer (Thermo Scientific, Inc.). The RNA integrity was checked by agarose gel electrophoresis.
Libraries were prepared using the Illumina TruSeq RNA Sample Preparation Kit v2 (Illumina, CA).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
Rsto_Raw_Read_Count_Matrix.csv
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| Data processing |
Quality trimming of raw reads was done with Sickle v1.33 with a threshold of 20.
Adapter trimming of raw reads was done with Scythe v.0.991 with a prior of 0.4
Bowtie2 2.3.4 was used to map the reads to the appropriate references with the following options: --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 ITAGv3.2 combined with either B. cinerea ASM83294v1, F. acuminatum (GGXD01000000), or R. stolonifer (GGWM01000000) transcriptomes for inoculated fruit samples. Pathogen transcriptomes alone were used for in vitro samples.
Supplementary_files_format_and_content: Bcin_Raw_Read_Count_Matrix.csv, Facu_Raw_Read_Count_Matrix.csv, Rsto_Raw_Read_Count_Matrix.csv: comma-separated files determined by mapping trimmed sequencing reads
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| Submission date |
Nov 15, 2018 |
| Last update date |
Dec 01, 2018 |
| 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) |
| GSE122555 |
Adaptation of necrotrophic infection strategies by Botrytis cinerea, Fusarium acuminatum, and Rhizopus stolonifer as a function of tomato fruit ripening |
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| Relations |
| BioSample |
SAMN10430672 |
| SRA |
SRX5010950 |
| 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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