biostudies-arrayexpressKorbinian BöslHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-6790In order to investigate the importance of FIP2 on bacterially induced gene regulation, we performed a targeted transcriptome profiling for immunologically relevant genes on RNA samples isolated from E. coli stimulated human macrophages from 7 donor treated with non-targeting and FIP2 silencing siRNA. Macrophages were stimulated for up to 4h with E.coli particles, RNA isolated and analyzed using Nanostring HS_Immunology_v2_C2328 probe set. The data was analyzed in R/Bioconductor 3.4.1/3.5 with limma 3.32.5biostudies-arrayexpressHybridization - According to the manufactures protocol. 65°C 18-20hLabeling - According to the manufactures protocol.Sample Collection - Human monocytes were isolated by plastic adherence from Lymphoprep (Axis‐Shield) separated buffycoats. Approval no. 2009/224 was received from the Regional Ethical Committee, Norwegian University of Science and Technology for the use of human blood and leukocytes. The monocytes were differentiated into macrophages in RPMI1640 supplemented with 50 ng/mL recombinant human M-CSF (#216-MC-025 R&D systems), 10 % pooled human A+ serum (The Blood Bank, St Olavs Hospital, Trondheim, Norway), 700 μM L-glutamine (Sigma-Aldrich) and 20 μg/mL Gensumycin (Sanofi-Aventis) at 37 oC and 5 % CO2. Medium was changed on day 3 and 5 after seeding.Sample Treatment - PBMC derived macrophages were transfected with 32 nM siRNA on day 6 and 8 after seeding using Lipofectamine®3000 Transfection Reagent (Invitrogen). Medium was changed to fresh antibiotic-free medium 2 h before the second siRNA transfection and the cells stimulated on day 10. The AllStars Negative Control siRNA (#SI03650318 QIAGEN) was used as a non-silencing control and Hs_RAB11FIP2_5 validated siRNA (QIAGEN) was used to target Rab11FIP2. pHrodo BioParticles (E. coli) were given to the cells in doses ranging from 7.5 to 30 particles per cell. BioParticles were sonicated and opsonized in medium with 10 % human serum for 5 min at 37 °C before beeing administered to the cells.Nucleic Acid Extraction - Total RNA was isolated from PBMC derived macrophages using QIAzol (Qiagen) and chloroform extraction followed by purification on RNeasy Mini columns, including DNAse digestion (Qiagen).Scaning - Count data was collected at maximum resolution.MIAME ScoreRaw DataOrganizationAssays and DataMAGE-TAB FilesArray DesignsData Transformation - Count data was imported to R/Bioconductor 3.4.1/3.5 using the NanoStringNorm 1.1.21 package without its internal normalization functions. Probes with counts in the range of the average of all non-targeting probes plus 2 standard deviations were excluded from further analysis. The count data was voom transformed and cyclic loess normalized.MetabolomicsUnknownTranscriptomicsGenomicsProteomicstranscription profiling by arrayHomo sapiensThe TLR4 adaptor TRAM controls phagocytosis of Gram-negative bacteria through the Rab11-family interacting protein 2Astrid Skjesol†, Mariia Yurchenko†, Lene Melsæther Grøvdal, Korbinian Bösl, Federica Agliano, Francesco Patane, Germana Lentini, Hera Kim, Giuseppe Teti, Richard K. Kandasamy, Bjørnar Sporsheim, Kristian K. Starheim, Douglas T. Golenbock, Harald Stenmark, Mary McCaffrey, Terje Espevik‡, Harald Husebye‡Richard KandasamyKorbinian BöslAstrid SkjesolHarald HusebyeTerje EspevikfalseNanostring profiling for immunologically relevant genes on RNA samples isolated from E. coli stimulated human FIP2 silenced macrophagesIn order to investigate the importance of FIP2 on bacterially induced gene regulation, we performed a targeted transcriptome profiling for immunologically relevant genes on RNA samples isolated from E. coli stimulated human macrophages from 7 donor treated with non-targeting and FIP2 silencing siRNA. Macrophages were stimulated for up to 4h with E.coli particles, RNA isolated and analyzed using Nanostring HS_Immunology_v2_C2328 probe set. The data was analyzed in R/Bioconductor 3.4.1/3.5 with limma 3.32.52019-03-08T00:00:00Z2022-03-14T19:26:45.133Z2022-03-14T19:26:45.133ZE-MTAB-6790EFO_0002768EFO_0002944EFO_0003814EFO_0003813EFO_0005518EFO_0003816EFO_0003815EFO_0003969