|
Status |
Public on Nov 10, 2013 |
Title |
G0 ex vivo CSF |
Sample type |
SRA |
|
|
Source name |
yeast cells
|
Organism |
Cryptococcus neoformans var. grubii |
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 |