|
| Status |
Public on Jul 29, 2023 |
| Title |
WT30_degrees_YPD_B |
| Sample type |
SRA |
| |
|
| Source name |
SN250
|
| Organism |
Candida albicans |
| Characteristics |
cell line: SN250
genotype: WT
treatment: YPD 30 degrees
|
| Treatment protocol |
Samples were normalized to expression from cells grown in YPD at 30 degrees C
|
| Growth protocol |
The reference strain SN250 and the corresponding rob1ΔΔ mutant were subjected to hyphal induction conditions using either Spider medium or RPMI at 37oC for 4 hr.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated with the MasterPure yeast RNA purification kit.
RNA TruSeq Kit was used for library construction
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Data processing |
Sequence reads were cleaned and adapter trimmed using trimmomatic-0.36
Each sample was mapped individually to the C. Albicans reference genome (SC5314 from NCBI) with STAR2.5.2b
Raw read counts were obtained using featurecounts from the subread1.5.0p3 package and SC5314 gene annotations using only uniquely aligned reads
DESeq2-1.14.1 within R-3.3.2 was used to perform data normalization and differential expression analysis with an adjusted p-value threshold of 0.05 on each set of raw expression measures.
Assembly: SC5314 from NCBI
Supplementary files format and content: tab-delimited text file containing raw counts for each sample
|
| |
|
| Submission date |
Jul 24, 2023 |
| Last update date |
Jul 29, 2023 |
| Contact name |
Damian Joseph Krysan |
| E-mail(s) |
damian-krysan@uiowa.edu
|
| Phone |
15853562270
|
| Organization name |
University of Iowa Department of Pediatrics
|
| Street address |
200 Hawkins Drive
|
| City |
Iowa City |
| State/province |
IA |
| ZIP/Postal code |
52242 |
| Country |
USA |
| |
|
| Platform ID |
GPL9133 |
| Series (1) |
| GSE238051 |
The Candida albicans reference strain SC5314 contains a rare, dominant allele of the transcription factor Rob1 that modulates biofilm formation and oral commensalism |
|
| Relations |
| BioSample |
SAMN36691857 |
| SRA |
SRX21134083 |
