|
| Status |
Public on Oct 13, 2022 |
| Title |
TF028indark2_CCTAAGS13L001R1_001 |
| Sample type |
SRA |
| |
|
| Source name |
TF028 knockout
|
| Organism |
Candida albicans |
| Characteristics |
strain: TF028 knockout
|
| Growth protocol |
Strains were grown on standard chamydospore inducing conditions (on corn meal agar with tween 80 under coerslips and incubated at room temperature in dark)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction was performed using Ribopure-Yeast RNA kit from Ambion
RNA-seq library was prepared using Lexogen’s quantseq 3' mRNA-Seq Library Prep Kit FWD as per Illumina user manual instructions
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Bluebee data analysis
In-house RNAseq pipeline was used for trimming and removal of low-quality tails using bbmap suite
STAR aligner with modified ENCODE settings was used for alignment to SC5314 genome
HTSeq-count with kit specific options (FWD) was used for gene count reading
DESeq2 was used to identify the differentially expressed genes
Assembly: Candida albicans SC5314 assembly 21
Supplementary files format and content: gene counts
|
| |
|
| Submission date |
Apr 14, 2022 |
| Last update date |
Oct 13, 2022 |
| Contact name |
Clarissa Jane Nobile |
| Organization name |
University of California, Merced
|
| Department |
Molecular and Cell Biology
|
| Lab |
Clarissa Nobile
|
| Street address |
5200 North Lake Rd
|
| City |
Merced |
| State/province |
CA |
| ZIP/Postal code |
95343 |
| Country |
USA |
| |
|
| Platform ID |
GPL24129 |
| Series (1) |
| GSE200778 |
A computational workflow for the analysis of 3’ Tag-Seq data |
|
| Relations |
| BioSample |
SAMN27578891 |
| SRA |
SRX14850209 |
