{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Allison Roberts"],"organism":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15742"],"description":["RNA-seq profiling of macrophages lacking Irf2, Irf9, or Irf2 and Irf9, as well as scramble controls was performed. Macrophages were infected with Listeria monocytogenes or uninfected under mock conditions and total RNA was harvested 2 hours post infection."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - Macrophages lacking Irf2, Irf9, or Irf2 and Irf9, as well as scramble controls were infected with Listeria monocytogenes or uninfected under mock conditions and total RNA was harvested 2 hours post infection. Three independent experiments were performed. Gene knockouts were generated via cas9 guide transduction into cas9-expressing cells.","Sequencing - Sequencing was performed by Novogene Corporation Inc. on an Illumina NovaSeq as paired-end 150 reads.","Nucleic Acid Extraction - Total RNA was isolated using TRIzol (Fisher) and Chloroform, and the PureLink RNA Mini Kit (12183018A, Ambion). RNA was then DNase I treated (NEB), and purified using RNA clean and concentrator columns (Zymo).","Library Construction - PolyA mRNA enrichment and library preparation was performed by Novogene Corporation Inc."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - The raw reads were pre-processed using HTStream (version 1.3.3) to filter out polyA tails, reads from PhiX, adapter sequences, reads that were too short (<50 bp), read ends with low quality (<Q20), and reads resulting from PCR duplication. The pre-processed reads were mapped to the Gencode M27 Mus musculus genome (GRCm39) and quantified using STAR aligner (version 2.7.9a). The R package edgeR was used to determine differentially expressed genes. Normalization was performed using trimmed mean of M-values."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA"],"species":["Mus musculus"],"pubmed_title":["Genome-wide screen in Mycobacterium tuberculosis infected macrophages reveals innate regulation of antibacterial mediators by IRF2"],"pubmed_authors":["Allison Roberts","Jeffery Cox","Allison W. Roberts, Linda N. Del Cid, Nicholas E. Garelis, Jeffery S. Cox"],"additional_accession":[]},"is_claimable":false,"name":"RNA-seq profiling of Listeria monocytogenes infected macrophages lacking Irf2, Irf9, or Irf2 and Irf9, as well as scramble controls","description":"RNA-seq profiling of macrophages lacking Irf2, Irf9, or Irf2 and Irf9, as well as scramble controls was performed. Macrophages were infected with Listeria monocytogenes or uninfected under mock conditions and total RNA was harvested 2 hours post infection.","dates":{"release":"2026-04-29T00:00:00Z","modification":"2026-04-29T01:01:54.745Z","creation":"2025-10-15T15:02:46.34Z"},"accession":"E-MTAB-15742","cross_references":{"ENA":["ERP182247"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"]}}