other:Article Title: Human Papillomavirus 16 E5 Inhibits Interferon Signaling and Supports Episomal Viral Maintenance
Article Snippet: 210 Proteomics array 211 The Phospho-Explorer Array (Full Moon Biosystems Cat #PEX100) was used according 212 to the manufacturer’s instructions.
Mass Spectrometry:Article Title: DksA is a conserved master regulator of stress response in Acinetobacter baumannii.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER VEGF Stem Cell Technologies 78127 FGF-2 RnD Systems 233FB025CF Aprotinin Med Chem Express P0017 Fibrin Sigma F3879 Thrombin Sigma T6884 Collagen I Devro 01APA006 Matrigel hESC-qualified Matrix, LDEV-Free Sigma CLS354277 Palmitate Sigma P0500 B27 Supplement ThermoFisher Scientific 17504044 B27 Supplement minus insulin ThermoFisher Scientific A1895601 DMEM, no glucose, no glutamine, no phenol red ThermoFisher Scientific A1443001 Insulin ThermoFisher Scientific 12585014 L-ascorbic acid 2-phosphate sesquimagnesium salt hydrate Sigma A8960-5G Phosphoexplorer Array Full Moon Biosystem PEX100 Interferon g Peprotech 300–02 IL-1b Peprotech 200-01B Poly(I:C) Sigma P9582 Endothelin-1 (TFA removed and QC for correct mass using mass spectrometry) GL Biochem (Shanghai) 55553 Bosentan Med Chem Express HY-A0013 Sitaxsentan Med Chem Express HY-11103 Deposited data Proteomics data of vascularised cardiac organoids This study PRIDE: PXD019266 RNA-seq of mouse heart maturation Quaife-Ryan et al.53 GEO: GSE95755 Single nuclei RNA-seq of human hearts Sim et al.12 GSE156707 Experimental Models: Cell Lines Human embryonic stem cell line HES3 WiCell RRID: CVCL_7158 Human embryonic stem cell line H9 WiCell RRID: CVCL_JL69 Human induced pluripotent stem cell line CRISPRi Gen1C 5 Mandegar et al.54 RRID: CVCL_VM38 Human induced pluripotent stem cell line AA CIMR hPSC Repository CW30382A Human induced pluripotent stem cell line CC CIMR hPSC Repository CW30318C Human induced pluripotent stem cell line HH CIMR hPSC Repository CW30171HH1 Human induced pluripotent stem cell line RM3.5 Kao et al.26 GAPTrap-BFP-IresMuro reporter line Experimental Models: Organisms/Strains C57BL/6J mice RRID: MGI: 3028467 Lama5pm mice Jones et al.30 N/A Oligonucleotides Primers for qPCR, see Table S1 N/A Software and Algorithms Image intensity analysis Mills et al.23 N/A Pole tracking analysis Mills et al.23 N/A MaxQuant v1.5.3.30 Cox and Mann55 RRID:SCR_014485 Perseus Tyanova and Cox56 RRID:SCR_015753 GENE-E or Morpheus Broad Institute N/A DAVID Huang et al. 2007 and Huang et al. 200957,58 RRID:SCR_001881 Enrichr https://maayanlab.cloud/Enrichr/ Chen et al.; Kuleshov et al. and Xie et al.59–61 N/A 16 Cell Reports 42, 112322, May 30, 2023 ..
RNA Sequencing:Article Title: DksA is a conserved master regulator of stress response in Acinetobacter baumannii.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER VEGF Stem Cell Technologies 78127 FGF-2 RnD Systems 233FB025CF Aprotinin Med Chem Express P0017 Fibrin Sigma F3879 Thrombin Sigma T6884 Collagen I Devro 01APA006 Matrigel hESC-qualified Matrix, LDEV-Free Sigma CLS354277 Palmitate Sigma P0500 B27 Supplement ThermoFisher Scientific 17504044 B27 Supplement minus insulin ThermoFisher Scientific A1895601 DMEM, no glucose, no glutamine, no phenol red ThermoFisher Scientific A1443001 Insulin ThermoFisher Scientific 12585014 L-ascorbic acid 2-phosphate sesquimagnesium salt hydrate Sigma A8960-5G Phosphoexplorer Array Full Moon Biosystem PEX100 Interferon g Peprotech 300–02 IL-1b Peprotech 200-01B Poly(I:C) Sigma P9582 Endothelin-1 (TFA removed and QC for correct mass using mass spectrometry) GL Biochem (Shanghai) 55553 Bosentan Med Chem Express HY-A0013 Sitaxsentan Med Chem Express HY-11103 Deposited data Proteomics data of vascularised cardiac organoids This study PRIDE: PXD019266 RNA-seq of mouse heart maturation Quaife-Ryan et al.53 GEO: GSE95755 Single nuclei RNA-seq of human hearts Sim et al.12 GSE156707 Experimental Models: Cell Lines Human embryonic stem cell line HES3 WiCell RRID: CVCL_7158 Human embryonic stem cell line H9 WiCell RRID: CVCL_JL69 Human induced pluripotent stem cell line CRISPRi Gen1C 5 Mandegar et al.54 RRID: CVCL_VM38 Human induced pluripotent stem cell line AA CIMR hPSC Repository CW30382A Human induced pluripotent stem cell line CC CIMR hPSC Repository CW30318C Human induced pluripotent stem cell line HH CIMR hPSC Repository CW30171HH1 Human induced pluripotent stem cell line RM3.5 Kao et al.26 GAPTrap-BFP-IresMuro reporter line Experimental Models: Organisms/Strains C57BL/6J mice RRID: MGI: 3028467 Lama5pm mice Jones et al.30 N/A Oligonucleotides Primers for qPCR, see Table S1 N/A Software and Algorithms Image intensity analysis Mills et al.23 N/A Pole tracking analysis Mills et al.23 N/A MaxQuant v1.5.3.30 Cox and Mann55 RRID:SCR_014485 Perseus Tyanova and Cox56 RRID:SCR_015753 GENE-E or Morpheus Broad Institute N/A DAVID Huang et al. 2007 and Huang et al. 200957,58 RRID:SCR_001881 Enrichr https://maayanlab.cloud/Enrichr/ Chen et al.; Kuleshov et al. and Xie et al.59–61 N/A 16 Cell Reports 42, 112322, May 30, 2023 ..
Real-time Polymerase Chain Reaction:Article Title: DksA is a conserved master regulator of stress response in Acinetobacter baumannii.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER VEGF Stem Cell Technologies 78127 FGF-2 RnD Systems 233FB025CF Aprotinin Med Chem Express P0017 Fibrin Sigma F3879 Thrombin Sigma T6884 Collagen I Devro 01APA006 Matrigel hESC-qualified Matrix, LDEV-Free Sigma CLS354277 Palmitate Sigma P0500 B27 Supplement ThermoFisher Scientific 17504044 B27 Supplement minus insulin ThermoFisher Scientific A1895601 DMEM, no glucose, no glutamine, no phenol red ThermoFisher Scientific A1443001 Insulin ThermoFisher Scientific 12585014 L-ascorbic acid 2-phosphate sesquimagnesium salt hydrate Sigma A8960-5G Phosphoexplorer Array Full Moon Biosystem PEX100 Interferon g Peprotech 300–02 IL-1b Peprotech 200-01B Poly(I:C) Sigma P9582 Endothelin-1 (TFA removed and QC for correct mass using mass spectrometry) GL Biochem (Shanghai) 55553 Bosentan Med Chem Express HY-A0013 Sitaxsentan Med Chem Express HY-11103 Deposited data Proteomics data of vascularised cardiac organoids This study PRIDE: PXD019266 RNA-seq of mouse heart maturation Quaife-Ryan et al.53 GEO: GSE95755 Single nuclei RNA-seq of human hearts Sim et al.12 GSE156707 Experimental Models: Cell Lines Human embryonic stem cell line HES3 WiCell RRID: CVCL_7158 Human embryonic stem cell line H9 WiCell RRID: CVCL_JL69 Human induced pluripotent stem cell line CRISPRi Gen1C 5 Mandegar et al.54 RRID: CVCL_VM38 Human induced pluripotent stem cell line AA CIMR hPSC Repository CW30382A Human induced pluripotent stem cell line CC CIMR hPSC Repository CW30318C Human induced pluripotent stem cell line HH CIMR hPSC Repository CW30171HH1 Human induced pluripotent stem cell line RM3.5 Kao et al.26 GAPTrap-BFP-IresMuro reporter line Experimental Models: Organisms/Strains C57BL/6J mice RRID: MGI: 3028467 Lama5pm mice Jones et al.30 N/A Oligonucleotides Primers for qPCR, see Table S1 N/A Software and Algorithms Image intensity analysis Mills et al.23 N/A Pole tracking analysis Mills et al.23 N/A MaxQuant v1.5.3.30 Cox and Mann55 RRID:SCR_014485 Perseus Tyanova and Cox56 RRID:SCR_015753 GENE-E or Morpheus Broad Institute N/A DAVID Huang et al. 2007 and Huang et al. 200957,58 RRID:SCR_001881 Enrichr https://maayanlab.cloud/Enrichr/ Chen et al.; Kuleshov et al. and Xie et al.59–61 N/A 16 Cell Reports 42, 112322, May 30, 2023 ..
Software:Article Title: DksA is a conserved master regulator of stress response in Acinetobacter baumannii.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER VEGF Stem Cell Technologies 78127 FGF-2 RnD Systems 233FB025CF Aprotinin Med Chem Express P0017 Fibrin Sigma F3879 Thrombin Sigma T6884 Collagen I Devro 01APA006 Matrigel hESC-qualified Matrix, LDEV-Free Sigma CLS354277 Palmitate Sigma P0500 B27 Supplement ThermoFisher Scientific 17504044 B27 Supplement minus insulin ThermoFisher Scientific A1895601 DMEM, no glucose, no glutamine, no phenol red ThermoFisher Scientific A1443001 Insulin ThermoFisher Scientific 12585014 L-ascorbic acid 2-phosphate sesquimagnesium salt hydrate Sigma A8960-5G Phosphoexplorer Array Full Moon Biosystem PEX100 Interferon g Peprotech 300–02 IL-1b Peprotech 200-01B Poly(I:C) Sigma P9582 Endothelin-1 (TFA removed and QC for correct mass using mass spectrometry) GL Biochem (Shanghai) 55553 Bosentan Med Chem Express HY-A0013 Sitaxsentan Med Chem Express HY-11103 Deposited data Proteomics data of vascularised cardiac organoids This study PRIDE: PXD019266 RNA-seq of mouse heart maturation Quaife-Ryan et al.53 GEO: GSE95755 Single nuclei RNA-seq of human hearts Sim et al.12 GSE156707 Experimental Models: Cell Lines Human embryonic stem cell line HES3 WiCell RRID: CVCL_7158 Human embryonic stem cell line H9 WiCell RRID: CVCL_JL69 Human induced pluripotent stem cell line CRISPRi Gen1C 5 Mandegar et al.54 RRID: CVCL_VM38 Human induced pluripotent stem cell line AA CIMR hPSC Repository CW30382A Human induced pluripotent stem cell line CC CIMR hPSC Repository CW30318C Human induced pluripotent stem cell line HH CIMR hPSC Repository CW30171HH1 Human induced pluripotent stem cell line RM3.5 Kao et al.26 GAPTrap-BFP-IresMuro reporter line Experimental Models: Organisms/Strains C57BL/6J mice RRID: MGI: 3028467 Lama5pm mice Jones et al.30 N/A Oligonucleotides Primers for qPCR, see Table S1 N/A Software and Algorithms Image intensity analysis Mills et al.23 N/A Pole tracking analysis Mills et al.23 N/A MaxQuant v1.5.3.30 Cox and Mann55 RRID:SCR_014485 Perseus Tyanova and Cox56 RRID:SCR_015753 GENE-E or Morpheus Broad Institute N/A DAVID Huang et al. 2007 and Huang et al. 200957,58 RRID:SCR_001881 Enrichr https://maayanlab.cloud/Enrichr/ Chen et al.; Kuleshov et al. and Xie et al.59–61 N/A 16 Cell Reports 42, 112322, May 30, 2023 ..
Transduction:
Protein-Protein interactions:Article Title: CCR9‐mediated signaling through β‐catenin and identification of a novel CCR9 antagonist
Article Snippet: AsPC‐1 cells were grown in RPMI1640 (Mediatech; Manassas, VA) with 10% FBS, 1% P/S, 1 mM sodium pyruvate (Gibco; Grand Island, NY) and 1% non‐essential amino acids (Irvine Scientific; Santa Ana, CA). .. To determine signaling pathways that were activated following exposure of MIAPaCa‐2 cells to CCL25, the Phospho Explorer Array (Full Moon Biosystems; Sunnyvale, CA) was used according to the manufacturer's protocol. ..
Extraction:
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