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| Status |
Public on Jul 23, 2023 |
| Title |
Mycelium, DMSO, rep3 |
| Sample type |
SRA |
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| Source name |
Fungal mycleium
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| Organism |
Botrytis cinerea |
| Characteristics |
tissue: Fungal mycleium
cell line: WT
strain: B05.10
treatment: DMSO
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| Growth protocol |
B. cinerea isolate B05.10 was cultured on potato dextrose agar (PDA, Oxoid) in a controlled-environment chamber at 20ºC under illumination with fluorescent light at a photo fluency rate of 12 μmol m-2 s-1 and 12/12 h photoperiod.
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA from B. cinerea B05.10 was extracted from clumps after 24 h growth on PDB supplemented with 0.25 mg mL-1 of Cyclo (Pro-Tyr), and DMSO as control, at 28ºC 150rpm, using NucleoSpin RNA Plant and Fungi kit (Macherey-Nagel), according to the manufacturer’s instructions.
For RNA sequencing analysis, 200-500 bp single-end read libraries were prepared using a TruSeq stranded total RNA kit (Illumina). The libraries were sequenced using a NextSeq550 instrument (Illumina).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Raw reads were preprocessed by NextSeq System Suite v.2.2.0. using specific NGS technology configuration parameters. This preprocessing removes low-quality, ambiguous and low-complexity stretches, linkers, adapters, vector fragments and contaminated sequences, and preserves the longest informative parts of the reads. SeqTrimNext also discarded sequences shorter than 25 bp.
Clean reads of the BAM files were aligned and annotated by Bowtie2 using the Botrytis cinerea B05.10 genome v.109.3 as the reference; these data were then sorted and indexed using SAMtools v.1.484110.
Uniquely localized reads were used to calculate the read number values for each gene by Sam2counts (https://github.com/vsbuffalo/sam2counts).
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| Submission date |
Jul 13, 2023 |
| Last update date |
Jul 23, 2023 |
| Contact name |
DAVID VELA-CORCIA |
| E-mail(s) |
dvela@uma.es
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| Organization name |
UNIVERSIDAD DE MALAGA
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| Department |
MICROBIOLOGIA
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| Street address |
CAMPUS DE TEATINOS
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| City |
MALAGA |
| ZIP/Postal code |
29010 |
| Country |
Spain |
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| Platform ID |
GPL24810 |
| Series (2) |
| GSE237225 |
Exploring the Impact of Cyclodipeptide on Fungal Metabolism: Insights into Membrane and Metabolic Responses [B. cinerea] |
| GSE237226 |
Exploring the Impact of Cyclodipeptide on Fungal Metabolism: Insights into Membrane and Metabolic Responses |
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| Relations |
| BioSample |
SAMN36426747 |
| SRA |
SRX21001680 |
| 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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