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Sample GSM1354905 Query DataSets for GSM1354905
Status Public on Mar 30, 2014
Title 5h-HUVEC.infected-Candida.WO1.rep1
Sample type SRA
 
Source name huvec infected
Organisms Candida albicans; Homo sapiens
Characteristics candida strain: WO1
infected human culture: HUVEC
time point: 5 hours
Growth protocol C. albicans cells were used to infect HUVEC cells or OKF6-TERT2 cells in tissue culture media for the indicated amount of time at 37 degrees celcius. The negative control samples were the host or C. albicans cells alone in tissue culture media for the indicated amount of time.
Extracted molecule total RNA
Extraction protocol RNA extractions were performed using RiboPure RNA Purification Kit, yeast (Life Technologies, AM1926) following manufacturer's protocols
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
 
Description SRX123583
18_5h_hc_w
Data processing Base calls were performed using the built-in Illumina basecaller
Sequenced reads were trimmed for adaptor sequence, and then mapped to Human GRCh38 whole genome reference and/or C. albicans SC5314 or WO1 reference using TopHat v1.4.0
Reads Per Kilobase of gene per Million mapped reads (RPKM) were calculated for each sample.
Differential expression of genes were computed between infected and uninfected samples
Genome_build: H. sapiens (GRCh38), C. albicans (sc5314; GCF_000182965.2), C. albicans (wo1; GCA_000149445.2)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample
 
Submission date Mar 21, 2014
Last update date May 15, 2019
Contact name Amol Carl Shetty
E-mail(s) ashetty@som.umaryland.edu
Organization name University of Maryland Baltimore
Department Institute for Genome Sciences
Street address 670 W. Baltimore Street, Floor 3
City Baltimore
State/province Maryland
ZIP/Postal code 21201
Country USA
 
Platform ID GPL18448
Series (2)
GSE56091 Characterization of transcriptome dynamics in response to contact with host cells [Phase I In Vitro]
GSE56093 Characterization of transcriptome dynamics in response to contact with host cells
Relations
BioSample SAMN02693701
SRA SRX123583

Supplementary file Size Download File type/resource
GSM1354905_18_5h_hc_w.C_albicans.rpkm.txt.gz 49.8 Kb (ftp)(http) TXT
GSM1354905_18_5h_hc_w.H_sapiens.rpkm.txt.gz 422.2 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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