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Sample GSM5403044 Query DataSets for GSM5403044
Status Public on Jan 12, 2022
Title 120_Blood-Cau_III
Sample type SRA
 
Source name fungal cells & whole blood
Organisms Homo sapiens; Candidozyma auris
Characteristics tissue: fungal cells & whole blood
fungal train: B8441
sex (h. sapiens): male
time: 120 min
donor: C
Treatment protocol 1000000/ml of Candida auris were used for infection of freshly drawn human whole blood
Growth protocol Candida auris preculture was prepared by growth over night in YPD at 30°C
Extracted molecule total RNA
Extraction protocol human RNA was isolated with PAXgene Blood RNA kit, fungal RNA was isolated with RiboPure RNA isolation kit yeast
After poly(A) filtering, mRNA was fragmented, and cDNA libraries were generated for each sample. 50 bp single sequence reads were produced using the Illumina HiSeq 2500 platform.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description C_auris_in_human-whole-blood_120min_donorC
Data processing quality controlled with FastQC (v0.11.8)
quality trimming of raw reads with Trimmomatic (v0.39)
rRNA depleted with SortMeRNA (v2.1b)
read alignment with HiSat2 (v2.1.0) against concatenated genomes
read counting with featureCounts (v1.34.0)
Genome_build: C. auris B8441 (s01-m01-r05)
Genome_build: H. sapiens genome GRCh38.p13 release 100.38
Supplementary_files_format_and_content: tab delimited text file with unnormalised C. auris read counts
Supplementary_files_format_and_content: tab delimited text file with unnormalised H. sapiens read counts
Supplementary_files_format_and_content: tab delimited text file with MRN normalised C. auris read counts
Supplementary_files_format_and_content: tab delimited text file with MRN normalised H. sapiens read counts
 
Submission date Jun 27, 2021
Last update date Jan 12, 2022
Contact name Sascha Schäuble
E-mail(s) sascha.schaeuble@leibniz-hki.de
Organization name Leibniz Institute for Natural Product Research and Infection Biology
Street address Beutenbergstraße 11a
City Jena
ZIP/Postal code 07745
Country Germany
 
Platform ID GPL30319
Series (1)
GSE179000 Candida auris infection of human whole blood
Relations
BioSample SAMN19907176
SRA SRX11239193

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

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