other:
Imaging:Article Title: OpenDVP: An experimental and computational framework for community-empowered deep visual proteomics
Article Snippet: .. Imaging was performed using Zeiss Axioscan 7. ..
Software:
Article Title:
Article Snippet: .. Software and code Policy information about availability of computer code Data collection Zeiss LSM 880 Zeiss black software Leica software (LAS X) Confocal laser scanning microscope (TCS SP8; Leica) Olympus ScanR Image Acquisition Software ImageQuant LAS 4000 for western blot AriaMx Real-Time PCR instrument (G8830A) for qPCRs Illumina Hiseq 4000 sequencer for ChIP-seq Comet Assay IV software (Perceptive Instruments, UK) Data analysis ImageJ/Fiji software (version 2.1.0/1.53c) Prism (version 8.4.2, GraphPad) Olympus ScanR Image Analysis Software (Version 3.0.1) Spotfire software (version 7.0.1; TIBCO 7.11) Comet Assay IV software (Perceptive Instruments, UK) Agilent AriaMx software (version 1.71) DESEQ2 for statistical analysis Bowtie2, MACS2, HOMER, deepTools For manuscripts utilizing custom algorithms or software that are central to the research but not yet described in published literature, software must be made available to editors and reviewers. ..
Staining:Article Title: Urolithin A-laden functional nanoparticles alleviate cisplatin-induced cardiotoxicity in mice by inhibiting inflammation-induced lymphangiogenesis.
Article Snippet: Following primary antibody incubation, the sections were treated with secondary antibodies: goat anti-mouse IgG Alexa Fluor-555 (catalog #A21425)/goat anti-rabbit IgG Alexa Fluor-488 (catalog #A-11070) at a 1:1000 dilution for 2 h. After incubation with secondary antibodies, the samples were washed three times with PBS and mounted using Vectashield with DAPI (catalog #H-2000-10, Vector Laboratories) for nuclear staining. .. The stained slides were visualized using a confocal microscope (LSM-900, Zeiss) or an Axioscan 7 (Zeiss). .. Images were obtained and processed using Zen Blue 3.3 software and quantified using ImageJ (NIH) or AngioTool64 software.
Microscopy:Article Title: Urolithin A-laden functional nanoparticles alleviate cisplatin-induced cardiotoxicity in mice by inhibiting inflammation-induced lymphangiogenesis.
Article Snippet: Following primary antibody incubation, the sections were treated with secondary antibodies: goat anti-mouse IgG Alexa Fluor-555 (catalog #A21425)/goat anti-rabbit IgG Alexa Fluor-488 (catalog #A-11070) at a 1:1000 dilution for 2 h. After incubation with secondary antibodies, the samples were washed three times with PBS and mounted using Vectashield with DAPI (catalog #H-2000-10, Vector Laboratories) for nuclear staining. .. The stained slides were visualized using a confocal microscope (LSM-900, Zeiss) or an Axioscan 7 (Zeiss). .. Images were obtained and processed using Zen Blue 3.3 software and quantified using ImageJ (NIH) or AngioTool64 software.
Article Title: The Integrated Stress Response Pathway Coordinates Translational Control of Multiple Immune Checkpoints in Lung Cancer
Article Snippet: Finally, slides were counterstained with 4′,6-diamidino-2-phenylindole (DAPI), and coverslips were mounted (ProLong Diamond, Invitrogen, P36961 ) and cured overnight before imaging. .. Slides were scanned at the UTSW Whole Brain Microscopy Facility on a Zeiss Axioscan 7. .. Finally, slides were counterstained with 4′,6-diamidino-2-phenylindole (DAPI), and coverslips were mounted (ProLong Diamond, Invitrogen, P36961 ) and cured overnight before imaging.
Laser-Scanning Microscopy:Article Title:
Article Snippet: .. Software and code Policy information about availability of computer code Data collection Zeiss LSM 880 Zeiss black software Leica software (LAS X) Confocal laser scanning microscope (TCS SP8; Leica) Olympus ScanR Image Acquisition Software ImageQuant LAS 4000 for western blot AriaMx Real-Time PCR instrument (G8830A) for qPCRs Illumina Hiseq 4000 sequencer for ChIP-seq Comet Assay IV software (Perceptive Instruments, UK) Data analysis ImageJ/Fiji software (version 2.1.0/1.53c) Prism (version 8.4.2, GraphPad) Olympus ScanR Image Analysis Software (Version 3.0.1) Spotfire software (version 7.0.1; TIBCO 7.11) Comet Assay IV software (Perceptive Instruments, UK) Agilent AriaMx software (version 1.71) DESEQ2 for statistical analysis Bowtie2, MACS2, HOMER, deepTools For manuscripts utilizing custom algorithms or software that are central to the research but not yet described in published literature, software must be made available to editors and reviewers. ..
Western Blot:Article Title:
Article Snippet: .. Software and code Policy information about availability of computer code Data collection Zeiss LSM 880 Zeiss black software Leica software (LAS X) Confocal laser scanning microscope (TCS SP8; Leica) Olympus ScanR Image Acquisition Software ImageQuant LAS 4000 for western blot AriaMx Real-Time PCR instrument (G8830A) for qPCRs Illumina Hiseq 4000 sequencer for ChIP-seq Comet Assay IV software (Perceptive Instruments, UK) Data analysis ImageJ/Fiji software (version 2.1.0/1.53c) Prism (version 8.4.2, GraphPad) Olympus ScanR Image Analysis Software (Version 3.0.1) Spotfire software (version 7.0.1; TIBCO 7.11) Comet Assay IV software (Perceptive Instruments, UK) Agilent AriaMx software (version 1.71) DESEQ2 for statistical analysis Bowtie2, MACS2, HOMER, deepTools For manuscripts utilizing custom algorithms or software that are central to the research but not yet described in published literature, software must be made available to editors and reviewers. ..
Real-time Polymerase Chain Reaction:Article Title:
Article Snippet: .. Software and code Policy information about availability of computer code Data collection Zeiss LSM 880 Zeiss black software Leica software (LAS X) Confocal laser scanning microscope (TCS SP8; Leica) Olympus ScanR Image Acquisition Software ImageQuant LAS 4000 for western blot AriaMx Real-Time PCR instrument (G8830A) for qPCRs Illumina Hiseq 4000 sequencer for ChIP-seq Comet Assay IV software (Perceptive Instruments, UK) Data analysis ImageJ/Fiji software (version 2.1.0/1.53c) Prism (version 8.4.2, GraphPad) Olympus ScanR Image Analysis Software (Version 3.0.1) Spotfire software (version 7.0.1; TIBCO 7.11) Comet Assay IV software (Perceptive Instruments, UK) Agilent AriaMx software (version 1.71) DESEQ2 for statistical analysis Bowtie2, MACS2, HOMER, deepTools For manuscripts utilizing custom algorithms or software that are central to the research but not yet described in published literature, software must be made available to editors and reviewers. ..
Chromatin Immunoprecipitation:Article Title:
Article Snippet: .. Software and code Policy information about availability of computer code Data collection Zeiss LSM 880 Zeiss black software Leica software (LAS X) Confocal laser scanning microscope (TCS SP8; Leica) Olympus ScanR Image Acquisition Software ImageQuant LAS 4000 for western blot AriaMx Real-Time PCR instrument (G8830A) for qPCRs Illumina Hiseq 4000 sequencer for ChIP-seq Comet Assay IV software (Perceptive Instruments, UK) Data analysis ImageJ/Fiji software (version 2.1.0/1.53c) Prism (version 8.4.2, GraphPad) Olympus ScanR Image Analysis Software (Version 3.0.1) Spotfire software (version 7.0.1; TIBCO 7.11) Comet Assay IV software (Perceptive Instruments, UK) Agilent AriaMx software (version 1.71) DESEQ2 for statistical analysis Bowtie2, MACS2, HOMER, deepTools For manuscripts utilizing custom algorithms or software that are central to the research but not yet described in published literature, software must be made available to editors and reviewers. ..
Single Cell Gel Electrophoresis:Article Title:
Article Snippet: .. Software and code Policy information about availability of computer code Data collection Zeiss LSM 880 Zeiss black software Leica software (LAS X) Confocal laser scanning microscope (TCS SP8; Leica) Olympus ScanR Image Acquisition Software ImageQuant LAS 4000 for western blot AriaMx Real-Time PCR instrument (G8830A) for qPCRs Illumina Hiseq 4000 sequencer for ChIP-seq Comet Assay IV software (Perceptive Instruments, UK) Data analysis ImageJ/Fiji software (version 2.1.0/1.53c) Prism (version 8.4.2, GraphPad) Olympus ScanR Image Analysis Software (Version 3.0.1) Spotfire software (version 7.0.1; TIBCO 7.11) Comet Assay IV software (Perceptive Instruments, UK) Agilent AriaMx software (version 1.71) DESEQ2 for statistical analysis Bowtie2, MACS2, HOMER, deepTools For manuscripts utilizing custom algorithms or software that are central to the research but not yet described in published literature, software must be made available to editors and reviewers. ..
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