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| Status |
Public on Sep 19, 2019 |
| Title |
CBS_Control_96h_II |
| Sample type |
SRA |
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| Source name |
CBS 118892 - Control - 96 hours, replicate II
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| Organism |
Trichophyton rubrum |
| Characteristics |
strain: CBS 118892
treatment: Control - 96 hours
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| Treatment protocol |
Approximately 10-6 conidia mL-1 was inoculated into 100 mL Sabouraud dextrose broth [SDB; 2% (w/v) glucose, 1% (w/v) peptone], and incubated under agitation at 28 °C for 96 h under agitation. Mycelia were aseptically transferred into 100 mL minimal medium (MM) at pH 5.0 containing 70 mM nitrate and either 50 mM glucose (control) or 0.5% (w/v) bovine keratin (treatment) as the carbon source. The cultures were incubated under agitation at 28 °C for 24 h, 48 h, or 96 h.
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| Growth protocol |
For RNA-seq libraries assembly, T. rubrum strain CBS118892 was maintained on malt extract agar [MEA; 2% (w/v) glucose, 2% (w/v) malt extract, 0.1% (w/v) peptone (w/v), pH 5.7] for 17 d at 28 °C.
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| Extracted molecule |
total RNA |
| Extraction protocol |
The obtained mycelium was harvested, frozen in liquid nitrogen, and stored at - 80 °C until RNA isolation was performed. Total RNA was isolated using an Illustra RNAspin mini isolation kit (GE Healthcare, Chicago, IL, USA) according to manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
DESeq2-96h.csv
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| Data processing |
FastQC v0.11.7 was used to visualize the libraries quality before and after trimming.
Trimmomatic v0.36 was used to remove adapters and quality filtered setting the cutoff threshold for average base quality score at 15 over a window of 4 bases. Reads shorter than 36 bases post-trimming were excluded.
Filtered reads were mapped onto the T. rubrum genome using the STAR v2.5.2b.
Gene level read-counts were quantified using STAR’s –quantMode GeneCounts parameter.
The data were analyzed using the R package DESeq2. The samples were normalized, and the dispersions were estimated using the default settings. The package was then used to identify differentially expressed genes for each pairwise comparison of interest. Genes with an adjusted P value of < 0.05 and a log2(foldchange) >= 1.5 (upregulation) or <= -1.5 (downregulation) were called as differentially expressed.
Genome_build: Broad T. rubrum strain CBS118892 genome
Supplementary_files_format_and_content: tab-delimited text files include reads count values for each sample and DESeq output in CSV format containing mean expression, fold changes and p value.
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| Submission date |
Jul 17, 2019 |
| Last update date |
Sep 19, 2019 |
| Contact name |
Pablo Rodrigo Sanches |
| E-mail(s) |
[email protected]
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| Organization name |
University of São Paulo
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| Department |
Genetics
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| Lab |
Molecular Biology and Genetics of fungi
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| Street address |
Av. Bandeirantes, 3900
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| City |
Ribeirão Preto |
| State/province |
SP |
| ZIP/Postal code |
14049-900 |
| Country |
Brazil |
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| Platform ID |
GPL23937 |
| Series (1) |
| GSE134406 |
Global Analysis of the dermatophyte Trichophyton rubrum when shifted from glucose to keratin |
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| Relations |
| SRA |
SRX6456203 |
| BioSample |
SAMN12306859 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3946075_geneCounts_CBS_Control_96h_II.txt.gz |
35.6 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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