|
| Status |
Public on Feb 25, 2021 |
| Title |
Strain U04 mrr1Δ +MRR1-Y813C+P1171P(t) control rep3 |
| Sample type |
SRA |
| |
|
| Source name |
Exponential phase yeast cultures
|
| Organism |
Clavispora lusitaniae |
| Characteristics |
strain: U04
genotype: mrr1delta +MRR1-Y813C+P1174P(t)
treatment: vehicle (water)
|
| Treatment protocol |
30 minutes treatment with vehicle (water), 0.5 mM diamide, or 0.5 mM hydrogen peroxide
|
| Growth protocol |
Overnight cultures grown in YPD at 30 C were back diluted into 5 ml YPD and grown at 37 C to mid-exponential phase on a roller drum, diluted into pre-warmed medium then grown, at 37 C, to mid-exponential phase again before 30 minutes treatment.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was harvested from snap-frozen pellets (using liquid nitrogen) using the MasterPure Yeast RNA Purification Kit (Epicentre)
Libraries were prepared using the Kapa mRNA HyperPrep Library Kit (Roche) following standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
U04 mrr1Δ +MRR1-Y813C+P1174P(t)
Fluconazole-sensitive, low Mrr1 activity, premature stop codon
U04.Y8P1.ctl.rep3
|
| Data processing |
Raw reads were aligned to genome (ATCC 42720) with gsnap (2018-02-05) spliced alignment
sam to bam conversion with picardtools (2.14.1)
bam to read counts using "featureCounts" from subread (1.6.0)
CPM file generated from DESeq2
Genome_build: candida_lusitaniae_ATCC42720_w_CBS_6936_MT (MT contamination fixed and MT genome assembled)
Supplementary_files_format_and_content: tab-delimited text file of read counts per feature and Experiment
Supplementary_files_format_and_content: csv-delimited text files of CPM normalized counts for each Experiment
|
| |
|
| Submission date |
Nov 25, 2020 |
| Last update date |
Feb 25, 2021 |
| Contact name |
Jason E Stajich |
| E-mail(s) |
jason.stajich@ucr.edu
|
| Organization name |
University of California, Riverside
|
| Department |
Microbiology & Plant Pathology
|
| Street address |
900 University Ave
|
| City |
Riverside |
| State/province |
CA - California |
| ZIP/Postal code |
92521 |
| Country |
USA |
| |
|
| Platform ID |
GPL24692 |
| Series (1) |
| GSE162151 |
Transcriptional profiling of strains with different levels of Mrr1 activity in Candida lusitaniae (RNA-Seq) |
|
| Relations |
| BioSample |
SAMN16912785 |
| SRA |
SRX9582527 |
