|
| Status |
Public on May 16, 2022 |
| Title |
mutant 50 uM Hemin biol rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
SC5314
|
| Organism |
Candida albicans |
| Characteristics |
cell line: SC5314
cell type: hap1 mutant
genotype: ura3-/- his1-/- arg4-/- leu2-/- hap1::NATr/hap1::LEU2 ADE2/ade2::URA3
treatment: YPD + 50 mM hemin 30'
|
| Treatment protocol |
At time 0, the cultures were split and 50 mM hemin was added to one half each.
|
| Growth protocol |
Overnight cultures grown in YPD were diluted to OD600=0.5 and grown another 2.5 hours
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using hot phenol.
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina, cat no. E7760, using 800ng total RNA as a starting material. mRNAs pull-down was performed using the Magnetic Isolation Module (NEB, cat no. E7490). After construction, the concentration of each library was measured using Qubit (Invitrogen) and the size was determined using the TapeStation 4200 with the High Sensitivity D1000 kit (cat no. 5067-5584).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
| |
|
| Description |
P2 flow cell
|
| Data processing |
Quality control was assessed using Fastqc (v0.11.8)
Reads were trimmed for adapters, low quality 3` and minimum length of 20 using CUTADAPT (v1.10).
100 bp single reads were aligned to a Candida_Albicans reference genome (GCF_000182965.3_ASM18296v3_genomic.fna from NCBI) using Tophat (v2.1.0, uses Bowtie2 version 2.2.6).
The number of reads per gene was counted using HTSeq-count (v2.2.0).
Assembly: GCF_000182965.3_ASM18296v3_genomic.fna from NCBI
Supplementary files format and content: The number of reads per gene was extracted into merged_counts.csv and normalized_counts.csv files for raw counts and normalized counts, respectively.
|
| |
|
| Submission date |
May 09, 2022 |
| Last update date |
Aug 15, 2022 |
| Contact name |
Daniel Kornitzer |
| E-mail(s) |
danielk@technion.ac.il
|
| Organization name |
Technion - IIT
|
| Department |
Faculty of Medicine
|
| Lab |
Kornitzer
|
| Street address |
1, Efron St
|
| City |
Haifa |
| ZIP/Postal code |
3109629 |
| Country |
Israel |
| |
|
| Platform ID |
GPL32241 |
| Series (1) |
| GSE202577 |
Effect of hemin and of HAP1 on C. albicans expression pattern |
|
| Relations |
| BioSample |
SAMN28164509 |
| SRA |
SRX15214068 |
