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| Status |
Public on Jan 01, 2022 |
| Title |
BB1_AGTCAA |
| Sample type |
SRA |
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| Source name |
Inoculated fruit
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| Organism |
Solanum lycopersicum |
| Characteristics |
genotype: Ailsa Craig
ripening stage: MG
treatment: Healthy
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| Extracted molecule |
total RNA |
| Extraction protocol |
At 3 dpi, fruit pericarp and epidermal tissue of the blossom end halves of healthy, mock-inoculated, and inoculated fruit were collected and immediately frozen in liquid nitrogen. Frozen tissue was ground to a fine powder in liquid nitrogen. 2 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 barcoded individually and analyzed for quantity and quality with the High Sensitivity DNA Analysis Kit in the Agilent 2100 Bioanalyzer (Agilent, USA). cDNA libraries were pooled in equal amounts for sequencing (single end, 50 bp) at the Expression Analysis Core Facility (UC Davis, CA, USA) in an Illumina HiSeq 2000 sequencer.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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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 B. cinerea 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
Supplementary_files_format_and_content: Read_counts.csv; comma-delimited file determined by mapping trimmed sequencing reads
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| Submission date |
Sep 09, 2021 |
| Last update date |
Jan 01, 2022 |
| 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) |
| GSE183836 |
Botrytis cinerea infection accelerates ripening and cell wall disassembly in tomato fruit to promote disease |
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| Relations |
| BioSample |
SAMN21370980 |
| SRA |
SRX12124988 |
| 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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