Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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RNA-seq of THP-1-derived macrophages infected with R. conorii and R. montanensis (1 hpi) against uninfected cells.

ABSTRACT: R. conorii (pathogenic) and R. montanensis (non-pathogenic) display opposite survival versus death phenotypes in macrophage-like cells, respectively. We herein employed a global transcriptomic profiling of host responses to infection (1hpi) of human THP-1 macrophages with R. conorii and R. montanensis. Shortly, total RNA was harvested from uninfected, R. conorii- and R. montanensis-infected THP-1 macrophages, DNA was removed from RNA purification (DNAse treatment), ribosomal RNA was depleted and cDNA libraries were constructed. The samples were sequenced using an Ion Proton V2 chip on Ion Chef Instrument. The programmes Cufflinks and Cuffmerge were used to map transcripts and calculate gene expression, and Cuffdiff was used to calculate which samples had genes, which were statistically significantly differentially expressed between conditions.

INSTRUMENT(S): Ion Torrent Proton

ORGANISM(S): Homo sapiens

SUBMITTER: Juan Martinez

PROVIDER: E-MTAB-6724 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:The early stages of the immune response against aberrant tissues such a tumors are technically difficult to study and therefore little understood. To analyze the innate immune response towards modified self-tissue we expressed a dominant-active version of the Ras oncogene in Drosophila imaginal discs and salivary glands. Signs of an immune response are observed on wings of adult flies, which show spots of melanization and in larvae, where the salivary glands attract blood cells. In line with the strong response mounted against salivary glands, they are found to express metalloproteases and apoptotic markers making them both accessible and recognizable for the immune system. The response against the glands bears several hallmarks of an encapsulation response including flattening of plasmatocytes, differentiation of lamellocytes, attachment of crystal cells and melanization at the final stage. RNA sequencing of the fat body, the primary producer of immune effectors, reveals a pattern of induced genes, which overlaps the one previously found upon wasp infestation but shows also several specific features. Evidence for the functional importance of one of the induced genes is presented proving the power of our approach to identify regulators of the response against modified self. Transcriptome analysis of the immune response in the fat body after expression of dominant-active RAS in the wing imaginal discs and salivary glands. Comparison of fat bodies from 3 control and 3 RAS-expressing larvae. For each sample fat bodies from 40 individuals were dissected. Differential gene expression files [output of Cuffdiff] are linked below: ResultsContr123vsRas123Individual.xls: Output file of Cuffdiff. Differential gene expression analysis, three control compared to individual Ras induced; replicate analysis using Cuffdiff. ResultsContr123vsRas123Multiple.xls: Output file of Cuffdiff. Differential gene expression analysis, three control compared to three Ras induced; replicate analysis using Cuffdiff. ResultsContr123vsRas12Multiple.xls: Output file of Cuffdiff. Differential gene expression analysis, three control compared to two Ras induced; replicate analysis using Cuffdiff.

Dataset Information

RNA-seq of THP-1-derived macrophages infected with R. conorii and R. montanensis (1 hpi) against uninfected cells.

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