|
| Status |
Public on Nov 10, 2013 |
| Title |
G0 ex vivo CSF |
| Sample type |
SRA |
| |
|
| Source name |
yeast cells
|
| Organism |
Cryptococcus neoformans |
| Characteristics |
strain: G0
condition: ex vivo cerebrospinal fluid (CSF)
tissue: yeast cells
|
| Growth protocol |
The in vivo CSF pellets were obtained from yeast cells directly harvested from patients' cerebrospinal fluid (CSF) by centrifugation and stored at -80C until RNA extraction. These samples were part of the Duke IRB approved Database and Specimen Repository for Infectious Disease Related Studies (PR0005314) in which patients are de-identified and clinical information is limited in collection. HC1 strain is from a patient in USA and strain G0 is from an Uganda patient. YPD broth (1% yeast extract, 1% Bacto Peptone, 2% dextrose) and sterile human CSF (pool of 10 -20 individuals) as previously described (59) were used for in vitro or ex vivo exposure of the strains. The strains were grown in YPD broth for 16 hours at 37¼C and then harvested. Additionally, yeast cells that reached stationary phase by culture in YPD overnight at 37¼C were then exposed to human CSF for 9 hours (CSF replenished every 3 hours) and then harvested. All harvested cells were snap frozen and lyophilized for total RNA isolation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs of the two strains (HC1 and G0) under the various treatments were extracted using TRI-zol (Invitrogen) according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Sequencing reads of each sample were mapped to C. neoformans var. grubii H99 (2012 release; http://www.ncbi.nlm.nih.gov/assembly/GCA_000149245.2/) using Tophat 2.0.0
HT-Seq count 0.5.3 (http://www-huber.embl.de/users/anders/HTSeq) was used to convert the mapped reads to read counts per gene.
DESeq package was used to normalize the read count for each gene among different samples
Genome_build: C. neoformans var. grubii H99 (2012 release; http://www.ncbi.nlm.nih.gov/assembly/GCA_000149245.2/)
Supplementary_files_format_and_content: tab-delimited text files include normlized expression level values for each Sample
|
| |
|
| Submission date |
Oct 23, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
John Perfect |
| E-mail(s) |
john.perfect@dm.duke.edu
|
| Organization name |
Duke University Medical Center
|
| Department |
Division of Infectious Disease
|
| Lab |
Perfect Lab
|
| Street address |
0557 Duke South, blue zone
|
| City |
Durham |
| State/province |
NC |
| ZIP/Postal code |
27710 |
| Country |
USA |
| |
|
| Platform ID |
GPL17123 |
| Series (1) |
| GSE51573 |
The Cryptococcus transcriptome at the site of human meningitis |
|
| Relations |
| BioSample |
SAMN02380729 |
| SRA |
SRX366937 |
