biostudies-arrayexpressRachelia WibawaHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-16655Legionella pneumophila is an intracellular pathogen that uses a type IV secretion system called Dot/Icm to translocate over 330 effector proteins into the infected cells. To explore the collective impact of Dot/Icm effectors on host cell processes, we created a library of 14 L. pneumophila genomic mutant strains lacking effector-rich regions (a total of 85 effector genes deleted) and used the multi-deletion mutants to interrogate host-pathogen interactions. We then performed bulk mRNAseq profilling of PMA-differentiated THP1 macrophages after infection with WT, Dot/Icm-deficient mutant, or genomic mutant strains of Legionella pneumophila 130b (18h post-infection, MOI 10).biostudies-arrayexpressLibrary Construction - After QC using Bioanalyzer, only samples with RIN >8.0 were used. The cDNA libraries for RNA sequencing were generated from 20 ng of RNA using an in-house multiplex RNA-seq method, where sample-specific indices were incorporated during oligo-d(T) priming of first strand cDNA (MHTP Medical Genomics Facility, https://doi.org/10.1038/s41467-021-23111-1).Sequencing - Sequencing was performed on NextSeq2000 (Illumina) using P3 50 cycle kit.Sample Collection - THP-1 cells were differentiated using PMA (50 ng/mL) for 3 days, then infected with either WT or mutant Lp 130b strains for 18h at MOI 10.Nucleic Acid Extraction - RNA was extracted using the IsolateII RNA Mini kit (Bioline) according to manufacturer's instruction.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesSequence Alignment - Parsing, base calling, adaptor trimming, and de-multiplexing were done using Dragen BCLConvert 3.7.4. Raw read files were named \"R1\", and the two indices files were named \"I1\" and \"I2\" respectively. The reads were then uploaded into the Galaxy platform for further analysis. After checking for the absence of any adaptors and low-quality reads using FastQC, reads were aligned to the Homo sapiens genome (GrCh38) using RNA-STAR. UMI de-duplication was done using UMI-tools deduplicate, and aligned reads were counted using featureCounts. Raw count files are provided (RawCounts.csv)Data Transformation - Genes with low expression (less than 10 counts in one sample, or less than 1 count per million across three samples) were filtered out. Data was normalized by CalcNormFactor using the Trimmed Mean of M-values (TMM) method and converted to log2 counts per million (log2 CPM) using cpm from the edgeR package. Filtered and normalised data was provided (FilteredNormLogCPM.csv).MetabolomicsUnknownTranscriptomicsGenomicsProteomicsNextSeq 2000RNA-seq of coding RNAHomo sapiensRachelia WibawaElizabeth HartlandfalseMulti-Dot/Icm effector deletion mutants reveal distinct host transcriptional responses in Legionella pneumophila infected macrophagesLegionella pneumophila is an intracellular pathogen that uses a type IV secretion system called Dot/Icm to translocate over 330 effector proteins into the infected cells. To explore the collective impact of Dot/Icm effectors on host cell processes, we created a library of 14 L. pneumophila genomic mutant strains lacking effector-rich regions (a total of 85 effector genes deleted) and used the multi-deletion mutants to interrogate host-pathogen interactions. We then performed bulk mRNAseq profilling of PMA-differentiated THP1 macrophages after infection with WT, Dot/Icm-deficient mutant, or genomic mutant strains of Legionella pneumophila 130b (18h post-infection, MOI 10).2026-02-28T00:00:00Z2026-05-29T20:55:13.045Z2026-02-16T17:26:23.274ZE-MTAB-16655ERP189205EFO_0002944EFO_0004170EFO_0004917EFO_0005518EFO_0003816EFO_0003738EFO_0004184