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A hallmark of the bradyzoite is the development of neuronal cysts that are resilient against host immune response and current therapeutics. The bradyzoite parasites within the cyst have a carbohydrate and protein-rich wall and a slow-replication cycle, allowing them to remain hidden from the host. The intracellular, encysted lifestyle of\n                      <jats:italic>T. gondii<\/jats:italic>\n                      has made them recalcitrant to molecular analysis in vivo.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      Here, we detail the results from transcriptional and proteomic analyses of bradyzoite-enriched fractions isolated from mouse brains infected with\n                      <jats:italic>T. gondii<\/jats:italic>\n                      over a time course of 21 to 150\u2009days. The enrichment procedure afforded consistent identification of over 2000 parasitic peptides from the mixed-organism sample, representing 366\u2009\n                      <jats:italic>T. gondii<\/jats:italic>\n                      proteins at 28, 90, and 120\u2009day timepoints. Deep sequencing of transcripts expressed during these three timepoints revealed that a subpopulation of genes that are transcriptionally expressed at a high level. Approximately one-third of these transcripts are more enriched during bradyzoite conditions compared to tachyzoites and approximately half are expressed at similar levels during each phase. The\n                      <jats:italic>T. gondii<\/jats:italic>\n                      transcript which increased the most over the course of chronic infection, sporoAMA1, shows stage specific isoform expression of the gene.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>\n                      We have expanded the transcriptional profile of in vivo bradyzoites to 120\u2009days post-infection and provided the first in vivo proteomic profile of\n                      <jats:italic>T. gondii<\/jats:italic>\n                      bradyzoites. The RNA sequencing depth of in vivo bradyzoite\n                      <jats:italic>T. gondii<\/jats:italic>\n                      was over 250-fold greater than previous reports and allowed us to identify low level transcripts and a novel bradyzoite-specific isoform of sporoAMA1.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s12864-019-6213-0","type":"journal-article","created":{"date-parts":[[2019,11,14]],"date-time":"2019-11-14T09:03:10Z","timestamp":1573722190000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":51,"title":["Proteomic and transcriptomic analyses of early and late-chronic Toxoplasma gondii infection shows novel and stage specific transcripts"],"prefix":"10.1186","volume":"20","author":[{"given":"Andrew L.","family":"Garfoot","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gary M.","family":"Wilson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joshua J.","family":"Coon","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9362-8088","authenticated-orcid":false,"given":"Laura J.","family":"Knoll","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2019,11,14]]},"reference":[{"key":"6213_CR1","doi-asserted-by":"publisher","first-page":"264","DOI":"10.1128\/CMR.05013-11","volume":"25","author":"F Robert-Gangneux","year":"2012","unstructured":"Robert-Gangneux F, Dard\u00e9 M-L. 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The University of Wisconsin is accredited by the International Association for Assessment and Accreditation of Laboratory Animal Care.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval"}},{"value":"NA.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare that they have no competing interests.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"859"}}