|
| Status |
Public on Apr 07, 2024 |
| Title |
cir1 in Yeast Nitrogen Base rep1 |
| Sample type |
SRA |
| |
|
| Source name |
fungal cell
|
| Organism |
Cryptococcus neoformans var. grubii H99 |
| Characteristics |
cell type: fungal cell
genotype: cir1 knockout
treatment: 6 hours YNB
|
| Treatment protocol |
Treatment was carried out over 6 hours in YPD with and without L-DOPA or in YNB with and without antimycin A. the cir1 knockout strain was only treated in YNB without antimycin A
|
| Growth protocol |
All strains were grown for 16 hours in YPD rich media at 30 degrees prior to a 6 hour treatment in YPD or YNB.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were flash frozen with liquid nitrogen and RNA was extracted using the Qiagen Rneasy protocol for yeast (mechanical disruption) followed by treatment with Dnase I (TURBO DNA-free™ Kit).
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
7_1
|
| Data processing |
illumina hiseq was used for basecalling
Sequenced reads were trimmed for adapter content using BBDuk and parameters ktrim=r k=23 mink=11
Trimmed sequences were then aligned (and genes counted) to the cryptococcus neoformans genome CNA3 via STAR version 2.7.6a with parameters --runMode alignReads --twopassMode Basic --quantMode GeneCounts --outSAMtype BAM Unsorted --outSAMunmapped Within
Counts were normalized during differential expression analysis via DESeq2’s median of ratios from Anders, S., & Huber, W. (2010).
Assembly: CNA3
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: Matrix table with normalized expression (DESeq2) information for each gene and every sample
|
| |
|
| Submission date |
Jan 10, 2023 |
| Last update date |
Apr 07, 2024 |
| Contact name |
James Kronstad |
| E-mail(s) |
kronstad@msl.ubc.ca
|
| Phone |
6048224732
|
| Organization name |
University of British Columbia
|
| Department |
Mircobiology and Immunology
|
| Lab |
Kronstad Lab
|
| Street address |
2185 E Mall
|
| City |
Vancouver |
| State/province |
BC |
| ZIP/Postal code |
V6T 1Z4 |
| Country |
Canada |
| |
|
| Platform ID |
GPL24579 |
| Series (1) |
| GSE222564 |
Characterizing the transcriptional role of L-DOPA and antimycin A on mitichondrial regulation in Cryptococcus neoformans using a cir1 knockout strain |
|
| Relations |
| BioSample |
SAMN32662838 |
| SRA |
SRX18991679 |
