|
| Status |
Public on Feb 16, 2021 |
| Title |
WT time 0 rep 33 |
| Sample type |
SRA |
| |
|
| Source name |
Yeast
|
| Organism |
Cryptococcus neoformans |
| Characteristics |
time point: 0 hours
genotype: Wild-type
replicate: 33
|
| Treatment protocol |
The cells were lysed by mechanical bead-beating, and the cell debris removed by centrifugation.
|
| Growth protocol |
Wild type and ∆Pdr802 strains were cultivated in DMEM for 24 hours at 37°C and 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction was performed by Trizol method.
The samples were sonicated to obtain fragments of about 200bp. Libraries were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina E7770L, following the manufactrer's instructions
RNAseq - Illumina NextSeq 1x75
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
The quality of the reads was evaluated by FastQC
Fastq files were aligned to the KN99 genome using NovoAlign
SAM files were converted to bam, reads were sorted and indexed, and read duplicates were removed from the final bam files using samtools
Samtools was also used to filter out reads with a mapping quality lesser than 20 phreds to guarantee single alignment of the reads. Read counts were assigned to specific genes with HTseq.
Differential expression was measured with DEseq2, p-values were adjusted using the IHW package.
Genome_build: Cryptococcus neoformans serotype A KN99 ASM221672v1
|
| |
|
| Submission date |
Dec 08, 2020 |
| Last update date |
Feb 16, 2021 |
| Contact name |
Daniel Paiva Agustinho |
| E-mail(s) |
daniel.molecular@gmail.com
|
| Organization name |
Washington University in St. Louis
|
| Department |
Molecular Microbiology
|
| Lab |
Doering Lab
|
| Street address |
660 S Euclid Ave
|
| City |
St Louis |
| State/province |
MO |
| ZIP/Postal code |
63110 |
| Country |
USA |
| |
|
| Platform ID |
GPL27451 |
| Series (1) |
| GSE162851 |
The transcription factor Pdr802 regulates Titan cell production and Cryptococcus neoformans pathogenicity (RNA-Seq) |
|
| Relations |
| BioSample |
SAMN17026667 |
| SRA |
SRX9650257 |
