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| Status |
Public on Jan 21, 2024 |
| Title |
sRNA Fo 60' light replicate 2 |
| Sample type |
SRA |
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| Source name |
Mycelium
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| Organism |
Fusarium oxysporum f. sp. lycopersici |
| Characteristics |
tissue: Mycelium
cell line: 4287
cell type: Hyphae
genotype: Wild type
treatment: Dark and 60' light
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| Treatment protocol |
Illumination was achieved with a set of four fluorescent tubes (Philips TL-D 18W/840) at a distance of ca. 60 cm, providing a light intensity of 0.25 m
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| Growth protocol |
As described in [Ruger-Herreros et al. 2019. BMC Genomics. 20: 67. doi:10.1186/s12864-019-5430-x; GEO Series accession number GSE107342]: 106 conidia were inoculated into 100 ml of DG medium in 500-ml Erlenmeyer flasks and incubated in the dark for three days in an orbital shaker. For illumination 25 ml samples of the cultures were transferred to Petri dishes under red safelight and incubated for one hour either in the dark or under white light The process with F. oxysporum was the same, except that the 3-day cultures were incubated in 145-mm Petri dishes with 80 ml of DGasn medium.
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA samples were extracted with Trizol (Invitrogen, Paisley, UK) using the protocol described by the manufacturer
Libraries constructed selecting transcripts with a size <150 nt from the total RNA samples described in [Ruger-Herreros et al. 2019. BMC Genomics. 20: 67. doi:10.1186/s12864-019-5430-x; GEO Series accession number GSE107342], in which the influence of light and CarS protein in F. fujikuroi and F. oxysporum transcriptomes was analyzed. They were sequenced on Illumina's Hiseq platform in mode 50 bp single read. Raw reads for all samples were trimmed, filtered, and quality controlled with AfterQC.
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| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
small RNA (<150 nt)
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| Data processing |
Raw reads for all samples were trimmed, filtered, and quality controlled with AfterQC.
Mapping of sRNA reads was done using Bowtie v1.1.1, designed to map short Illumina reads of ~35 nt, or Bowtie2 v2.2.9 for longer reads.
The gff annotation files from both fungi were used to extract fasta files, containing coding, intronic, and intergenic sequences. The extraction was done after creating the corresponding features with the genome browser Artemis 16.0.0.
Assembly: EF1.27 (fusarium fujikuroi)
Assembly: FO2.27 (fusarium oxysporum)
Supplementary files format and content: Ff_sense_raw_read_counts.csv: Raw reads in Fusarium fujikuroi genes in sense orientation, csv format
Supplementary files format and content: Ff_antisense_raw_read_counts.csv: Raw reads in Fusarium fujikuroi genes in antisense orientation, csv format
Supplementary files format and content: Fo_sense_raw_read_counts.csv: Raw reads in Fusarium oxysporum genes in sense orientation, csv format
Supplementary files format and content: Fo_antisense_raw_read_counts.csv: Raw reads in Fusarium oxysporum genes in antisense orientation, csv format
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| Submission date |
Jan 12, 2024 |
| Last update date |
Jan 21, 2024 |
| Contact name |
Javier Avalos |
| E-mail(s) |
[email protected]
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| Phone |
+34 954557110
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| Organization name |
Universidad de Sevilla
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| Department |
Genetica
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| Street address |
Av. Reina Mercedes sn
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| City |
Sevilla |
| ZIP/Postal code |
41012 |
| Country |
Spain |
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| Platform ID |
GPL34083 |
| Series (2) |
| GSE253160 |
Evidence of small interfering RNA in the fungus Fusarium fujikuroi (miRNA-Seq) |
| GSE253166 |
Evidence of small interfering RNA in the fungus Fusarium fujikuroi |
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| Relations |
| BioSample |
SAMN39423250 |
| SRA |
SRX23203676 |
| 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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