|
| Status |
Public on Feb 01, 2021 |
| Title |
JMB77 in Plasma rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
Liquid Culture
|
| Organism |
Candida parapsilosis |
| Characteristics |
growth medium: Plasma
strain: JMB77
|
| Growth protocol |
Isolates were confirmed as C. parapsilosis sensu stricto using PCR probes specific to the ITS1 region. Yeast were grown overnight in YPD medium (1% yeast extract, 2% peptone, 2% dextrose) with vigorous agitation at 37°C. Stationary phase cultures were washed with sterile water, and resuspended in fresh YPD medium, tissue culture medium M199 (BioWhittaker/Lonza #BW12-117Q) or pooled human blood plasma (sodium heparin anticoagulated) at 3 x 106 / ml, and further incubated at 37°C for 3 hours without shaking. Under these growth conditions, filaments (hyphae or pseudohyphae) were not observed. Parallel samples were tested in adhesion assays to confirm the adhesive phenotype, or yeast were centrifuged, and pellets flash frozen in liquid N2, and stored at -80° C for later RNA extraction for RNA seq or qPCR validation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from each and purified using RiboPure Yeast extraction kit (Ambion/Life Technologies). RNA integrity was assessed using agarose gels and Agilent Bioanalyzer.
RNA-seq library preparation and sequencing of extracted total RNA was performed following ribosomal RNA depletion using paired end reads (Illumina HiSeq2000), 2x150 bp, from all samples.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Adhesive isolate JMB77 grown in adhesion inducing medium: Plasma at 37 degrees C
|
| Data processing |
Raw sequence quality control and trimming was performed with FastQC v0.11.5 and Skewer v0.2.1
Reads were simultaneously aligned to the CDC317 C. parapsilosis reference genome and quantified using Salmon v1.0.0 in mapping-based mode
Gene-level expression values in quant files were imported into DESeq2 v1.18.1 R package using the tximport v1.6.0 R package
DESeq2 v1.18.1 R package was used to run differential expression analysis
Genome_build: CDC317
Supplementary_files_format_and_content: Salmon quant files containing gene level expression counts which have been corrected for gc content and sequence-specific random hexamer priming biases
|
| |
|
| Submission date |
Oct 08, 2020 |
| Last update date |
Feb 02, 2021 |
| Contact name |
Alper Uzun |
| E-mail(s) |
auzun@wihri.org
|
| Organization name |
Women and Infants Hospital of Rhode Island
|
| Department |
Pediatrics
|
| Street address |
200 Chestnut St.
|
| City |
Providence |
| State/province |
RI |
| ZIP/Postal code |
02903 |
| Country |
USA |
| |
|
| Platform ID |
GPL18663 |
| Series (1) |
| GSE159274 |
Transcription Profiles Associated with Inducible Adhesion in Candida parapsilosis |
|
| Relations |
| BioSample |
SAMN16400379 |
| SRA |
SRX9267472 |
