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Deciphering this complex temporal and spatial interplay is crucial for improved diagnostics and therapeutics. However, the technical limitations of existing methods of expression profiling, such as microarray analysis, significantly reduce their utility for obtaining both bacterial and host expression profiles from infected cells. We developed the heterogeneous RNA-Seq (hRNA-Seq) method to simultaneously capture prokaryotic and eukaryotic expression profiles of bacteria-infected cells. As proof of principle, hRNA-Seq was applied to \u003cem\u003eChlamydia\u003c/em\u003e-infected cells, successfully obtaining the transcriptomes of both \u003cem\u003eChlamydia\u003c/em\u003e and their host cells at 1 and 24 hours post-infection. Substantial transcription was found in the immediate-early period of infection for both \u003cem\u003eChlamydia\u003c/em\u003e and the host cell. Numerous novel host responses were found; in particular we discovered putative positive feedback mechanisms for \u003cem\u003eChlamydia\u003c/em\u003e-induced fibrotic scarring.","descriptionType":"Abstract"}],"geoLocations":[],"fundingReferences":[],"xml":"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","url":"https://figshare.com/articles/dataset/Simultaneous_transcriptional_profiling_of_Chlamydia_and_their_host_cells_by_heterogenous_RNA_Seq_hRNA_Seq_/723377/1","contentUrl":null,"metadataVersion":1,"schemaVersion":"http://datacite.org/schema/kernel-4","source":"mds","isActive":true,"state":"findable","reason":null,"viewCount":2,"viewsOverTime":[{"yearMonth":"2025-05","total":1},{"yearMonth":"2025-05","total":1}],"downloadCount":0,"downloadsOverTime":[{"yearMonth":"2025-05","total":0},{"yearMonth":"2025-05","total":0}],"referenceCount":0,"citationCount":0,"citationsOverTime":[],"partCount":0,"partOfCount":0,"versionCount":0,"versionOfCount":0,"created":"2016-01-18T14:29:35.000Z","registered":"2016-01-18T14:29:36.000Z","published":"2013","updated":"2025-06-01T03:40:02.000Z"},"relationships":{"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