|
| Status |
Public on Feb 08, 2023 |
| Title |
BG2_ctrl_2 |
| Sample type |
SRA |
| |
|
| Source name |
BG2
|
| Organism |
Nakaseomyces glabratus |
| Characteristics |
strain: BG2
genotype: WT
treatment: control
|
| Treatment protocol |
Co-cultur: Candida glabrata (starting OD600 =0.1) and L. fermentum (starting OD600=0.05) were incubated in MRS medium at 37°C. 80 rpm for 10 hours; single culture: C. glabrata ( starting OD600=0.1) was inucabated at 37°C, 80rpm for 10 hours.
|
| Growth protocol |
Candida glabrata isolates were grown in MRS medium at 37°C, 180rpm overnight. L. fermentum was grown at 37°C, 80rpm overnight.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Phenol Chloroform extraction was performed for RNA extraction
NEB mRNA Libraby preparation with poly-A enrichtment
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
resBG2_deseq2.csv
|
| Data processing |
Demultiplexing with bcl2fastq v2.20.0.422
Reads were mapped against reference with bowtie2
Read count was done with Rsubread (default settings)
normalization, filtering of the counted reads and differential gene expression was performed via DESeq2 (rows with <10 counts were filtered out; rest default settings)
Assembly: Candida glabrata CBS183
Supplementary files format and content: comma-limited file with results of differential gene expression (log2Foldchange), one file per comparison
|
| |
|
| Submission date |
May 10, 2022 |
| Last update date |
Feb 08, 2023 |
| Contact name |
Isabella Zangl |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Natural Resources and Life Sciences, Vienna
|
| Department |
Insitute for Microbial Genetics
|
| Street address |
Konrad Lorenz Str. 24
|
| City |
Tulln an der Donau |
| ZIP/Postal code |
3430 |
| Country |
Austria |
| |
|
| Platform ID |
GPL25492 |
| Series (1) |
| GSE202656 |
Limosilactobacillus fermentum Limits Candida glabrata Growth by Ergosterol Depletion |
|
| Relations |
| BioSample |
SAMN28177825 |
| SRA |
SRX15224970 |
