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Sample GSM1354948 Query DataSets for GSM1354948
Status Public on Mar 30, 2014
Title kidney_infected_Candida_12h.rep1
Sample type SRA
 
Source name Kidney
Organisms Candida albicans; Mus musculus
Characteristics mouse strain: BALB/c
candida strain background: SC5314
strain genotype/variation: wild type
tissue: Kidney
timepoint: 12 Hours
Growth protocol C. albicans cells were either injected into the tail vein of a mouse or swabbed onto the tongue of a anesthetized mouse.
Extracted molecule total RNA
Extraction protocol RNA was isolated from the infected mouse tissues using the Qiagen Rneasy mini kit (Cat#74104)
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 SRX339584
Data processing Base calls were performed using the built-in Illumina basecaller
Sequenced reads were trimmed for adaptor sequence, and then mapped to Mouse (GRCm38.70 + NT_096355 + NT_095534) whole genome reference using TopHat v1.4.0 and/or C. albicans SC5314 using Bowtie v0.12.9
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: M.musculus (GRCm38.70 + NT_096355 + NT_095534), C. albicans (sc5314)
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 GPL18449
Series (2)
GSE56092 Characterization of transcriptome dynamics in response to contact with host cells [Phase II In Vivo]
GSE56093 Characterization of transcriptome dynamics in response to contact with host cells
Relations
BioSample SAMN02693672
SRA SRX339584

Supplementary file Size Download File type/resource
GSM1354948_kidney_CW696_12h_1.C_albicans.rpkm.txt.gz 39.5 Kb (ftp)(http) TXT
GSM1354948_kidney_CW696_12h_1.M_musculus.rpkm.txt.gz 269.9 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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