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LPS and LPS\u2009+\u2009IFN\u03b3 are stimuli that are widely used to activate microglia. However, the transcriptomic profiles of microglia treated with LPS and LPS\u2009+\u2009IFN\u03b3 have not been properly compared. Here, we treated murine primary microglial cultures with LPS or LPS\u2009+\u2009IFN\u03b3 for 6\u2009hours and then performed RNA-Sequencing. Gene expression patterns induced by the treatments were obtained by WGCNA and 11 different expression profiles were found, showing differential responses to LPS and LPS\u2009+\u2009IFN\u03b3 in many genes. Interestingly, a subset of genes involved in Parkinson\u2019s, Alzheimer\u2019s and Huntington\u2019s disease were downregulated by both treatments. By DESeq analysis we found differentially upregulated and downregulated genes that confirmed LPS and LPS\u2009+\u2009IFN\u03b3 as inducers of microglial pro-inflammatory responses, but also highlighted their involvement in specific cell functions. In response to LPS, microglia tended to be more proliferative, pro-inflammatory and phagocytic; whereas LPS\u2009+\u2009IFN\u03b3 inhibited genes were involved in pain, cell division and, unexpectedly, production of some inflammatory mediators. In summary, this study provides a detailed description of the transcriptome of LPS- and LPS\u2009+\u2009IFN\u03b3 treated primary microglial cultures. It may be useful to determine whether these <jats:italic>in vitro<\/jats:italic> phenotypes resemble microglia in <jats:italic>in vivo<\/jats:italic> pathological conditions.<\/jats:p>","DOI":"10.1038\/s41598-018-34412-9","type":"journal-article","created":{"date-parts":[[2018,10,25]],"date-time":"2018-10-25T09:38:18Z","timestamp":1540460298000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":52,"title":["RNA-Seq transcriptomic profiling of primary murine microglia treated with LPS or LPS\u2009+\u2009IFN\u03b3"],"prefix":"10.1038","volume":"8","author":[{"given":"Marta","family":"Pulido-Salgado","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5667-4133","authenticated-orcid":false,"given":"Jose M.","family":"Vidal-Taboada","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9713-3795","authenticated-orcid":false,"given":"Gerardo Garcia-Diaz","family":"Barriga","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carme","family":"Sol\u00e0","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5601-4466","authenticated-orcid":false,"given":"Josep","family":"Saura","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2018,10,31]]},"reference":[{"key":"34412_CR1","doi-asserted-by":"publisher","first-page":"R506","DOI":"10.1016\/j.cub.2008.04.047","volume":"18","author":"D Soulet","year":"2008","unstructured":"Soulet, D. & Rivest, S. Microglia. Current biology: CB 18, R506\u2013508, https:\/\/doi.org\/10.1016\/j.cub.2008.04.047 (2008).","journal-title":"Current biology: CB"},{"key":"34412_CR2","doi-asserted-by":"publisher","first-page":"169","DOI":"10.1177\/1073858414530512","volume":"21","author":"D Gomez-Nicola","year":"2015","unstructured":"Gomez-Nicola, D. & Perry, V. H. Microglial dynamics and role in the healthy and diseased brain: a paradigm of functional plasticity. The Neuroscientist: a review journal bringing neurobiology, neurology and psychiatry 21, 169\u2013184, https:\/\/doi.org\/10.1177\/1073858414530512 (2015).","journal-title":"The Neuroscientist: a review journal bringing neurobiology, neurology and psychiatry"},{"key":"34412_CR3","doi-asserted-by":"publisher","first-page":"145","DOI":"10.1016\/j.cyto.2008.01.006","volume":"42","author":"YC Lu","year":"2008","unstructured":"Lu, Y. C., Yeh, W. C. & Ohashi, P. S. LPS\/TLR4 signal transduction pathway. 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