{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Sascha Schäuble"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16334"],"description":["This study investigates how the echinocandin antifungal drug caspofungin (CAS) modulates early immune responses during Candida albicans bloodstream infection. Echinocandin-susceptible (ECHS/FKSwt) and echinocandin-resistant (ECHR/FKSmut) C. albicans candidemia strains were used to determine whether CAS-induced host transcriptional changes depend on fungal susceptibility. Because immune modulation by CAS appears highly context dependent, we used an ex vivo human whole-blood system to capture physiologically relevant immune-pathogen interactions.   Fresh human whole blood from healthy donors was infected ex vivo with either an echinocandin-susceptible (ECHS/FKSwt) or echinocandin-resistant (ECHR/FKSmut) C. albicans isolate. Samples were treated with CAS or left untreated as controls. After a defined incubation period, leukocyte RNA was isolated. Human mRNA sequencing was performed by Novogene (Novogene GmbH, Munich). RNA quality was assessed prior to library preparation, and globin mRNA was removed using GlobinClear. Sequencing was performed on an Illumina platform using 150 bp paired-end reads. Raw sequencing data underwent standard quality control, including removal of adapter sequences and low-quality reads. Clean reads were aligned to the human reference genome, and gene expression was quantified. Differential expression analyses were performed to identify host transcriptional responses to CAS during infections with susceptible versus resistant C. albicans strains."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Library Construction - Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.","Sample Collection - Human peripheral blood was collected from healthy volunteers with written informed consent. This study was conducted in accordance with the Declaration of Helsinki and all protocols were approved by the Ethics Committee of the University Hospital Jena (permit number: 3639-12/12).","Sequencing - Preprocessing of raw reads including quality control and gene abundance estimation was done with the GEO2RNaseq pipeline (v0.9.12) in R (version 3.5.1). Quality analysis was done with FastQC (v0.11.8) before and after trimming. Read-quality trimming was done with Trimmomatic (v0.36). Reads were rRNA-filtered using SortMeRNA (v2.1) with a single rRNA database combining all rRNA databases shipped with SortMeRNA. Reference annotation was created by extracting and combining exon features from corresponding annotation files. Reads were mapped against the reference genome of H. sapiens (Hsapiens_GRCh38p14) using HiSat2 (v2.1.0, paired-end mode). Gene abundance estimation was done with featureCounts (v1.28.0) in paired-end mode with default parameters. MultiQC version 1.7 was finally used to summarize and assess the quality of the output of FastQC, Trimmomatic, HiSat, featureCounts, and SAMtools. The count matrix with gene abundance data with and without median-of-ratios normalization (MRN) were extracted.","Nucleic Acid Extraction - After 8 hours of infection, human RNA was stabilized in PAXgene Blood RNA tubes (PreAnalytiX) and extracted using the PAXgene Blood RNA Isolation Kit (PreAnalytiX) according to the manufacturer’s instructions. RNA concentration was measured with a NanoDrop OneC spectrophotometer (Thermo Fisher Scientific), and RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies)."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Median-of-ratios normalization (MRN) was used to normalize raw sequencing reads."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA"],"species":["Homo sapiens"],"pubmed_title":["Caspofungin enhances antifungal immunity in human blood through transcriptional reprogramming"],"pubmed_authors":["Aia Shehata, Sascha Schäuble, Grit Walther, Gianni Panagiotou, Oliver Kurzai, Kerstin Hünniger-Ast","Sascha Schäuble"],"additional_accession":[]},"is_claimable":false,"name":"Caspofungin enhances antifungal immunity in human blood through transcriptional reprogramming","description":"This study investigates how the echinocandin antifungal drug caspofungin (CAS) modulates early immune responses during Candida albicans bloodstream infection. Echinocandin-susceptible (ECHS/FKSwt) and echinocandin-resistant (ECHR/FKSmut) C. albicans candidemia strains were used to determine whether CAS-induced host transcriptional changes depend on fungal susceptibility. Because immune modulation by CAS appears highly context dependent, we used an ex vivo human whole-blood system to capture physiologically relevant immune-pathogen interactions.   Fresh human whole blood from healthy donors was infected ex vivo with either an echinocandin-susceptible (ECHS/FKSwt) or echinocandin-resistant (ECHR/FKSmut) C. albicans isolate. Samples were treated with CAS or left untreated as controls. After a defined incubation period, leukocyte RNA was isolated. Human mRNA sequencing was performed by Novogene (Novogene GmbH, Munich). RNA quality was assessed prior to library preparation, and globin mRNA was removed using GlobinClear. Sequencing was performed on an Illumina platform using 150 bp paired-end reads. Raw sequencing data underwent standard quality control, including removal of adapter sequences and low-quality reads. Clean reads were aligned to the human reference genome, and gene expression was quantified. Differential expression analyses were performed to identify host transcriptional responses to CAS during infections with susceptible versus resistant C. albicans strains.","dates":{"release":"2026-01-31T00:00:00Z","modification":"2026-05-27T18:00:20.507Z","creation":"2025-12-01T15:53:03.107Z"},"accession":"E-MTAB-16334","cross_references":{"ENA":["ERP185906"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"]}}