|
| Status |
Public on Mar 30, 2021 |
| Title |
NRH5045_aCSF |
| Sample type |
SRA |
| |
|
| Source name |
yeast cell
|
| Organism |
Cryptococcus neoformans |
| Characteristics |
isolate: NRH5045
strain: VNBI
condition: Artificial CSF
day: Day1
repeat: Rep1
|
| Growth protocol |
(1) aCSF: yeast cells incubated in aCSF at 37oC for 24 hours. Cells were harvested by centrifugation at 3000 RPM and stored at -800C. (2) rCSF: yeast cells were inoculated intracisternally into 2-3 kg New Zealand White rabbits receiving daily cortisone acetate. Each yeast strain was inoculated into three separate rabbits. Rabbit CSF was withdrawn (1-2ml) after 24 and 96 hours in the rabbit subarachnoid space. rCSF containing the same strain were pooled, centrifuged to pellet the cells and the cell pellets were stored at -800C. (3) YPD / CAP: yeast cells were grown for 24 hours in yeast peptone dextrose broth (YPD) or capsule-inducing media (CAP), centrifuged to collect the cell pellet, and store at -800C. (4) Human CSF (hCSF): yeasts per ml of CSF (1-5mls) was directly withdrawn under a lumbar puncture as standard of care, centrifuged to pellet and stored at -80C until RNA isolation was performed.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
These lyophilized samples were treated with Trizol and total RNA was extracted using the Qiagen RNeasy Mini Kit according to the manufacturer's instructions.
Library preparation was prepared by shearing the RNA and adapted for Illumina sequencing using the TruSeq RNA Library Preparation Kit (Illumina, San Diego, CA) for YPD and CAP conditions or the Tag-Seq Protocol (Shishkin et al Nat Methods 2015) for the in vivo CSF and aCSF samples.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
The quality filtering and adaptor trimming were performed using Cutadapt (v 1.12).
Paired-read alignment for RNA-seq data was carried out against the gene set for C. neoformans var. grubii H99 (CNA3) excluding non-coding RNAs and mitochondria genes, using STAR (v 2.5.3a).
The expected count, TPM, and FPKM for each gene were estimated with RSEM (v1.2.31).
Genome_build: CNA3 (GCA_000149245.3)
Supplementary_files_format_and_content: Tab-delimited text files include length, Effective length, Expected count, TPM, and FPKM For each gene.
|
| |
|
| Submission date |
Mar 29, 2021 |
| Last update date |
Mar 30, 2021 |
| Contact name |
John R. Perfect |
| E-mail(s) |
john.perfect@duke.edu
|
| Organization name |
Duke University School of Medicine
|
| Department |
Division of Infectious Diseases
|
| Lab |
John Perfect
|
| Street address |
303 Research Drive, Rm.337
|
| City |
Durham |
| State/province |
North Carolina |
| ZIP/Postal code |
27705 |
| Country |
USA |
| |
|
| Platform ID |
GPL27451 |
| Series (1) |
| GSE171092 |
The Cryptococcal Central Nervous System Transcriptome during Human Disease |
|
| Relations |
| BioSample |
SAMN18528173 |
| SRA |
SRX10469459 |
