|
| Status |
Public on Dec 21, 2018 |
| Title |
Wt_Cu_R3 |
| Sample type |
SRA |
| |
|
| Source name |
Yeast cells
|
| Organism |
Zygosaccharomyces bailii |
| Characteristics |
strain: IST302
genotype: wild-type
|
| Growth protocol |
Yeast strains were batch cultured at 30°C, with orbital agitation (250 rpm), in liquid mineral medium (MM) containing: 0.17% (w/v) yeast nitrogen base (YNB) and 2% (v/v) glucose, at pH 4.0, and supplemented with CuSO4 (0.08 mM final concentration).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction was performed by using a modified hot phenol method, described in Amin-ul Mannan et., Analytical Biochemistry, 2009.
Libraries were prepared using the QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
Wt_Cu.txt
Mut_Wt_Cu.txt
|
| Data processing |
Quality trimming of the sequences performed using BBDuk
Sequence reads were aligned to the Z. bailii IST302 genome assembly using the alignment algorithm STAR v2.5.2a, using the recommended parameters in QuantSeq 3' mRNA-Seq Integrated Data Analysis Pipeline on Bluebee platform
Quantification of reads per gene was performed using the htseq-count script of the HTSeq suite, in the intersection nonempty mode
Differential gene expression analysis was conducted using the Bioconductor software package edgeR
Genome_build: GCA_900162805.1 assembly deposited in ENA
Supplementary_files_format_and_content: text file with logFC, logCPM, FDR
|
| |
|
| Submission date |
Apr 23, 2018 |
| Last update date |
Dec 21, 2018 |
| Contact name |
Isabel Sá-Correia |
| E-mail(s) |
isacorreia@tecnico.ulisboa.pt
|
| Organization name |
Instituto Superior Técnico
|
| Department |
Department of Bioengineering
|
| Lab |
iBB-Institute for Bioengineering and Biosciences
|
| Street address |
Avenida Rovisco Pais, 1
|
| City |
Lisbon |
| ZIP/Postal code |
1049-001 |
| Country |
Portugal |
| |
|
| Platform ID |
GPL24921 |
| Series (1) |
| GSE113552 |
Transcriptional profiling of Zygosaccharomyces bailii early response to acetic acid or copper stresses mediated by ZbHaa1 |
|
| Relations |
| BioSample |
SAMN08971740 |
| SRA |
SRX3989063 |
