NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1248608 Query DataSets for GSM1248608
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

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap