{"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-15110"],"description":["We confronted moDCs with wildtype (WT) HCMV TB40E BAC4 or ΔUL111A (HCMV lacking CMVIL-10) with an MOI of 3 and/or A. fumigatus germ tubes with an MOI of 0.5 for 9 h, either individually (single infection) or simultaneously (co-infection), and performed RNA-seq. moDCs were incubated with or without 50 ng/mL recombinant CMVIL-10 for 24 h prior to challenge with A. fumigatus for 9 h and performed RNA-Seq."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - Monocyte-derived dendritic cells (moDCs) were generated from CD14+ monocytes isolated from peripheral blood mononuclear cell as previously described.  Seelbinder B, Wallstabe J, Marischen L, Weiss E, Wurster S, Page L, Löffler C, Bussemer L, Schmitt A-L, Wolf T, Linde J, Cicin-Sain L, Becker J, Kalinke U, Vogel J, Panagiotou G, Einsele H, Westermann AJ, Schäuble S, Loeffler J. 2020. Triple RNA-Seq Reveals Synergy in a Human Virus-Fungus Co-infection Model. Cell Reports 33:108389.  Guinan J, Lopez BS. 2020. Generating Bovine Monocyte-Derived Dendritic Cells for Experimental and Clinical Applications Using Commercially Available Serum-Free Medium. Frontiers in Immunology Volume 11 - 2020.","Nucleic Acid Extraction - Total RNA from the samples was isolated according to the manufacturer’s instructions. An on-column DNase digestion step was included in the RNA isolation protocol. RNA extraction kit: RNeasy Mini/Micro Kit (Qiagen) Elution volume: 40 µl","Library Construction - Library preparation was performed with the NEBNext® Poly(A) mRNA Magnetic Isolation Module and NEBNext® UltraTM II Directional mRNA kit (New England Biolabs) according to the manufacturer’s instructions (2). The protocol starts with a poly(A) RNA selection step using Oligo dT Beads d(T). The mRNA was fragmented and samples were then introduced  into a reverse transcription to generate first strand cDNA. After the second strand cDNA  synthesis, 3’-ends were adenylated and sequencing adapters were ligated. Those comprise  sequencing primer- and flow cell-binding sites, as well as indices for multiplexed sequencing  of pooled libraries. Adapter-ligated fragments were amplified during a 15-cycle PCR reaction. Universal Human Reference RNA (UHR) was simultaneously processed as internal positive  control (PosC) but discarded after successful library validation.","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 A. fumigatus (Af293, ASM265v1) using HiSat2 (v2.1.0, single-end mode). Gene abundance estimation was done with featureCounts (v1.28.0) in single-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."],"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":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA"],"species":["Homo sapiens"],"pubmed_authors":["Sascha Schäuble"],"additional_accession":[]},"is_claimable":false,"name":"Unveiling immune interference: How dendritic cell response to co-infection with Aspergillus fumigatus is modulated by human cytomegalovirus and its virokine CMVIL10","description":"We confronted moDCs with wildtype (WT) HCMV TB40E BAC4 or ΔUL111A (HCMV lacking CMVIL-10) with an MOI of 3 and/or A. fumigatus germ tubes with an MOI of 0.5 for 9 h, either individually (single infection) or simultaneously (co-infection), and performed RNA-seq. moDCs were incubated with or without 50 ng/mL recombinant CMVIL-10 for 24 h prior to challenge with A. fumigatus for 9 h and performed RNA-Seq.","dates":{"release":"2025-09-09T00:00:00Z","modification":"2025-09-09T13:24:01.474Z","creation":"2025-05-02T11:50:39.387Z"},"accession":"E-MTAB-15110","cross_references":{"ENA":["ERP172207"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"]}}