|
| Status |
Public on Sep 27, 2019 |
| Title |
Wt_Flu_II |
| Sample type |
SRA |
| |
|
| Source name |
Wild type_Flc
|
| Organism |
Nakaseomyces glabratus |
| Characteristics |
strain: KUE100
genotype/variation: Wild type
treatment: 1h fluconazole exposure
|
| Growth protocol |
Cells were grown in minimal medium and exposed to fluconazole stress for 1h or not (control). Cells were pelleted and frozen at -80ºC until RNA extraction
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Ambion Ribopure-Yeast RNA kit, according to the manufacturer's instructions
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
Sequenced reads were trimmed for adaptor sequence, low-quality base calls using Skewer v0.2.2 with parameters -m pe -l 36 -q 15 -Q 15
Reads were mapped to CBS138 whole genome using TopHat v2.1.1 with parameters -p 12 -g 1 --b2-very-sensitive --library-type fr-firststrand
Reads counts per feature (ORF) were obtained with the htseq-count script from HTSeq (v 0.7.1) using parameters -m union -s reverse -t gene -i Name
Genome_build: CBS138 (http://www.candidagenome.org/)
Supplementary_files_format_and_content: Table with read counts for each feature (ORF)
|
| |
|
| Submission date |
Apr 04, 2019 |
| Last update date |
Jan 19, 2022 |
| Contact name |
Miguel Cacho Teixeira |
| Organization name |
Instituto Superior Tecnico
|
| Department |
Institute for Bioengineering and Biosciences
|
| Street address |
Avenida Rovisco Pais 1
|
| City |
Lisbon |
| ZIP/Postal code |
1049-001 |
| Country |
Portugal |
| |
|
| Platform ID |
GPL26394 |
| Series (1) |
| GSE129349 |
Expression profilling of C. glabrata response to fluconazole and the role of the transcription factor Rpn4 in such response |
|
| Relations |
| BioSample |
SAMN11347124 |
| SRA |
SRX5643907 |
