|
| Status |
Public on Jan 20, 2021 |
| Title |
Wild Type 2 |
| Sample type |
SRA |
| |
|
| Source name |
yeast cells
|
| Organism |
Candida albicans |
| Characteristics |
strain: SC5314
genotype: WT
|
| Growth protocol |
Strains were grown overnight in YPD shaking at 30°C. The following day they were diluted 1:100 in YPD and grown for three hours shaking at 30°C.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Cells were broken by hot phenol and RNA was purified using the RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturers instructions. Samples were treated with TURBO DNase (Invitrogen GmbH, Darmstadt, Germany) to remove any residual genomic DNA, and remaining RNA was cleaned by a second purification using the RNeasy Mini kit.
Further steps to prepare for and conduct RNA sequencing were done by Eurofins Genomics (Konstanz, Germany). Such steps included purification of poly(A) mRNA molecules, mRNA fragmentation, preparation of strand-specific cDNA libraries, adapter ligation, and Illumina (HiSeq 2500) sequencing (single reads, 1x 50 base pair length).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Adapter and low quality end trimming using Trimmomatic (v0.36)
Mapping of reads to Candida albicans SC5314 genome assembly 22 using STAR (v2.6.1b) to produce BAM files
Raw read counts per feature generated using HTSeq (v0.6.1)
Normallization and determination of differentially expressed genes using DESeq2 (v1.14.1)
Genome_build: Candida albicans assembly 22
Supplementary_files_format_and_content: Processed data files for individual samples are tab delimited text files containing feature identifier (systematic orf name) and read counts
|
| |
|
| Submission date |
Jan 19, 2021 |
| Last update date |
Jan 20, 2021 |
| Contact name |
Joachim Morschhäuser |
| E-mail(s) |
joachim.morschhaeuser@uni-wuerzburg.de
|
| Organization name |
University of Würzburg
|
| Department |
Institute for Molecular Infection Biology
|
| Street address |
Josef-Schneider-Str 2, Bau D15
|
| City |
Würzburg |
| ZIP/Postal code |
97080 |
| Country |
Germany |
| |
|
| Platform ID |
GPL19036 |
| Series (1) |
| GSE165091 |
Investigation of the transcriptional effect of artificial activation of Czf1 in Candida albicans |
|
| Relations |
| BioSample |
SAMN17380043 |
| SRA |
SRX9895436 |
