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| Status |
Public on Dec 01, 2018 |
| Title |
IV4 |
| Sample type |
SRA |
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| Source name |
In vitro fungal culture
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| Organism |
Fusarium acuminatum |
| Characteristics |
ripening stage: N/A
days post inoculation: N/A
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| Extracted molecule |
total RNA |
| Extraction protocol |
Fungal RNA from the in vitro cultures was extracted using TRIzol (Invitrogen) and purified using the Quick-RNA MiniPrep Kit (Zymo Research).
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 |
Facu_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 |
GPL25818 |
| 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 |
SAMN10430663 |
| SRA |
SRX5010959 |
| 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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