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z-stack from previously published chrx-46plex oligofisseq dataset  (Nikon)


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    Structured Review

    Nikon z-stack from previously published chrx-46plex oligofisseq dataset
    Z Stack From Previously Published Chrx 46plex Oligofisseq Dataset, supplied by Nikon, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/z+stack+datasets/pmc11239506-178-41-70
    Average 90 stars, based on 1 article reviews
    z-stack from previously published chrx-46plex oligofisseq dataset - by Bioz Stars, 2026-09
    90/100 stars

    Images

    Related Articles

    Fluorescence:

    Article Title: Deconwolf enables high-performance deconvolution of widefield fluorescence microscopy images
    Article Snippet: The nomenclature is the same as in ref. . CT, layer 6 corticothalamic neurons; IT, intratelencephalic neurons; NP, near-projecting neurons; OPC, oligodendrocyte precursor cells; PVALB, parvalbumin-expressing neurons; SST, somatostatin-expressing neurons; VIP, vasoactive intestinal peptide-expressing neurons. c , Maximum z-projection of a z-stack from the previously published ChrX-46plex OligoFISSEQ dataset , without deconvolution (Raw) or after deconvolution with DW or with the deconvolution module in the commercial software NIS Elements AR (Nikon) (NIS).

    Article Title: Metformin and Inhibition of Transforming Growth Factor-Beta Stimulate In Vitro Transport in Primary Renal Tubule Cells
    Article Snippet: Renal cells on transwell membranes were stained for NKCC2 and ZO-1 immunofluorescence was also imaged on a Nikon structured illumination microscope (SIM) as a Z-stack at 0.12-μm thickness using a × 100 total internal reflection fluorescence objective.

    Article Title: Endothelial Cell Selectivity to Nanoparticles Depends on Mechanical Phenotype
    Article Snippet: To confirm the endocytosis of the red dye-loaded (excitation/emission wavelengths: 580/605) carboxylatemodified polystyrene 100 nm NPs, fluorescence images of the cells were taken under a super-resolution microscope, Z-stack (Nikon).

    Article Title: Transcription bodies regulate gene expression by sequestering CDK9
    Article Snippet: Multiposition, z -stack (20 μm in 41 steps, NIDAQ Piezo Z) timelapse (2 min time interval) imaging was performed with a Nikon ×60/1.2 Plan Apochromat VC water objective.

    Article Title: Endogenous Extracellular Matrix Regulates the Response of Osteosarcoma 3D Spheroids to Doxorubicin.
    Article Snippet: Images were acquired with a 25× water-immersion objective and multi-photon excitation fluorescence, resonant scanning, zoom at 1, and line average of 4 for a total of 100 slices on the Z-stack (A1R MP confocal microscope, Nikon).

    Article Title: SARS-CoV-2 infection induces DNA damage, through CHK1 degradation and impaired 53BP1 recruitment, and cellular senescence
    Article Snippet: A z -stack was acquired every minute for 100 min total using a 60× oil-immersion objective (Nikon Plan Apo VC, 1.4 numerical aperture).

    Article Title: Host Retromer Protein Sorting Nexin 2 Interacts with Human Respiratory Syncytial Virus Structural Proteins and is Required for Efficient Viral Production
    Article Snippet: The cell nuclei staining was omitted. (E) HRSV infected and transfected with Vps4-GFP plasmid. (F) PLA for HRSV N and Vps4-GFP performed in HRSV-infected cells and transfected with Vps4-GFP plasmid. (G) A merge between panels E and F. (H) HRSV-infected cells stained for TGN46. (I) PLA performed in HRSV-infected cells without using the HRSV N primary antibody as a biological control of the experiment. (J) Merge between panels H and I. (K) TGN46 in HRSV-infected cells. (L) PLA for HRSV F and N proteins. (M) Merge of panels K and L. (N) Proximity/interaction of F and N occurs at the Golgi compartment; approximately 35% of the cells analyzed showed PLA positive staining as in panels L and M. The plot profile in panel N was performed following the arrow traced in panel M. Panels A to D represent a single plane from a Z-stack imaging from a Nikon N-SIM microscope (superresolution imaging), while E to M represent a single focal plane of two independent experiments taken with a Zeiss 780 confocal microscope.

    Article Title: SARS-CoV-2 infection induces DNA damage, through CHK1 degradation and impaired 53BP1 recruitment, and cellular senescence.
    Article Snippet: A z-stack was acquired every minute for 100 min total using a 60× oil-immersion objective (Nikon Plan Apo VC, Nature Cell Biology Article https://doi.org/10.1038/s41556-023-01096-x 1.4 numerical aperture).

    Super-Resolution Microscopy:

    Article Title: Deconwolf enables high-performance deconvolution of widefield fluorescence microscopy images
    Article Snippet: The nomenclature is the same as in ref. . CT, layer 6 corticothalamic neurons; IT, intratelencephalic neurons; NP, near-projecting neurons; OPC, oligodendrocyte precursor cells; PVALB, parvalbumin-expressing neurons; SST, somatostatin-expressing neurons; VIP, vasoactive intestinal peptide-expressing neurons. c , Maximum z-projection of a z-stack from the previously published ChrX-46plex OligoFISSEQ dataset , without deconvolution (Raw) or after deconvolution with DW or with the deconvolution module in the commercial software NIS Elements AR (Nikon) (NIS).

    Article Title: Metformin and Inhibition of Transforming Growth Factor-Beta Stimulate In Vitro Transport in Primary Renal Tubule Cells
    Article Snippet: Renal cells on transwell membranes were stained for NKCC2 and ZO-1 immunofluorescence was also imaged on a Nikon structured illumination microscope (SIM) as a Z-stack at 0.12-μm thickness using a × 100 total internal reflection fluorescence objective.

    Article Title: Endothelial Cell Selectivity to Nanoparticles Depends on Mechanical Phenotype
    Article Snippet: To confirm the endocytosis of the red dye-loaded (excitation/emission wavelengths: 580/605) carboxylatemodified polystyrene 100 nm NPs, fluorescence images of the cells were taken under a super-resolution microscope, Z-stack (Nikon).

    Article Title: Transcription bodies regulate gene expression by sequestering CDK9
    Article Snippet: Multiposition, z -stack (20 μm in 41 steps, NIDAQ Piezo Z) timelapse (2 min time interval) imaging was performed with a Nikon ×60/1.2 Plan Apochromat VC water objective.

    Article Title: Endogenous Extracellular Matrix Regulates the Response of Osteosarcoma 3D Spheroids to Doxorubicin.
    Article Snippet: Images were acquired with a 25× water-immersion objective and multi-photon excitation fluorescence, resonant scanning, zoom at 1, and line average of 4 for a total of 100 slices on the Z-stack (A1R MP confocal microscope, Nikon).

    Article Title: SARS-CoV-2 infection induces DNA damage, through CHK1 degradation and impaired 53BP1 recruitment, and cellular senescence
    Article Snippet: A z -stack was acquired every minute for 100 min total using a 60× oil-immersion objective (Nikon Plan Apo VC, 1.4 numerical aperture).

    Article Title: Host Retromer Protein Sorting Nexin 2 Interacts with Human Respiratory Syncytial Virus Structural Proteins and is Required for Efficient Viral Production
    Article Snippet: The cell nuclei staining was omitted. (E) HRSV infected and transfected with Vps4-GFP plasmid. (F) PLA for HRSV N and Vps4-GFP performed in HRSV-infected cells and transfected with Vps4-GFP plasmid. (G) A merge between panels E and F. (H) HRSV-infected cells stained for TGN46. (I) PLA performed in HRSV-infected cells without using the HRSV N primary antibody as a biological control of the experiment. (J) Merge between panels H and I. (K) TGN46 in HRSV-infected cells. (L) PLA for HRSV F and N proteins. (M) Merge of panels K and L. (N) Proximity/interaction of F and N occurs at the Golgi compartment; approximately 35% of the cells analyzed showed PLA positive staining as in panels L and M. The plot profile in panel N was performed following the arrow traced in panel M. Panels A to D represent a single plane from a Z-stack imaging from a Nikon N-SIM microscope (superresolution imaging), while E to M represent a single focal plane of two independent experiments taken with a Zeiss 780 confocal microscope.

    Article Title: SARS-CoV-2 infection induces DNA damage, through CHK1 degradation and impaired 53BP1 recruitment, and cellular senescence.
    Article Snippet: A z-stack was acquired every minute for 100 min total using a 60× oil-immersion objective (Nikon Plan Apo VC, Nature Cell Biology Article https://doi.org/10.1038/s41556-023-01096-x 1.4 numerical aperture).

    Microscopy:

    Article Title: Deconwolf enables high-performance deconvolution of widefield fluorescence microscopy images
    Article Snippet: The nomenclature is the same as in ref. . CT, layer 6 corticothalamic neurons; IT, intratelencephalic neurons; NP, near-projecting neurons; OPC, oligodendrocyte precursor cells; PVALB, parvalbumin-expressing neurons; SST, somatostatin-expressing neurons; VIP, vasoactive intestinal peptide-expressing neurons. c , Maximum z-projection of a z-stack from the previously published ChrX-46plex OligoFISSEQ dataset , without deconvolution (Raw) or after deconvolution with DW or with the deconvolution module in the commercial software NIS Elements AR (Nikon) (NIS).

    Article Title: Metformin and Inhibition of Transforming Growth Factor-Beta Stimulate In Vitro Transport in Primary Renal Tubule Cells
    Article Snippet: Renal cells on transwell membranes were stained for NKCC2 and ZO-1 immunofluorescence was also imaged on a Nikon structured illumination microscope (SIM) as a Z-stack at 0.12-μm thickness using a × 100 total internal reflection fluorescence objective.

    Article Title: Endothelial Cell Selectivity to Nanoparticles Depends on Mechanical Phenotype
    Article Snippet: To confirm the endocytosis of the red dye-loaded (excitation/emission wavelengths: 580/605) carboxylatemodified polystyrene 100 nm NPs, fluorescence images of the cells were taken under a super-resolution microscope, Z-stack (Nikon).

    Article Title: Transcription bodies regulate gene expression by sequestering CDK9
    Article Snippet: Multiposition, z -stack (20 μm in 41 steps, NIDAQ Piezo Z) timelapse (2 min time interval) imaging was performed with a Nikon ×60/1.2 Plan Apochromat VC water objective.

    Article Title: Endogenous Extracellular Matrix Regulates the Response of Osteosarcoma 3D Spheroids to Doxorubicin.
    Article Snippet: Images were acquired with a 25× water-immersion objective and multi-photon excitation fluorescence, resonant scanning, zoom at 1, and line average of 4 for a total of 100 slices on the Z-stack (A1R MP confocal microscope, Nikon).

    Article Title: SARS-CoV-2 infection induces DNA damage, through CHK1 degradation and impaired 53BP1 recruitment, and cellular senescence
    Article Snippet: A z -stack was acquired every minute for 100 min total using a 60× oil-immersion objective (Nikon Plan Apo VC, 1.4 numerical aperture).

    Article Title: Host Retromer Protein Sorting Nexin 2 Interacts with Human Respiratory Syncytial Virus Structural Proteins and is Required for Efficient Viral Production
    Article Snippet: The cell nuclei staining was omitted. (E) HRSV infected and transfected with Vps4-GFP plasmid. (F) PLA for HRSV N and Vps4-GFP performed in HRSV-infected cells and transfected with Vps4-GFP plasmid. (G) A merge between panels E and F. (H) HRSV-infected cells stained for TGN46. (I) PLA performed in HRSV-infected cells without using the HRSV N primary antibody as a biological control of the experiment. (J) Merge between panels H and I. (K) TGN46 in HRSV-infected cells. (L) PLA for HRSV F and N proteins. (M) Merge of panels K and L. (N) Proximity/interaction of F and N occurs at the Golgi compartment; approximately 35% of the cells analyzed showed PLA positive staining as in panels L and M. The plot profile in panel N was performed following the arrow traced in panel M. Panels A to D represent a single plane from a Z-stack imaging from a Nikon N-SIM microscope (superresolution imaging), while E to M represent a single focal plane of two independent experiments taken with a Zeiss 780 confocal microscope.

    Article Title: SARS-CoV-2 infection induces DNA damage, through CHK1 degradation and impaired 53BP1 recruitment, and cellular senescence.
    Article Snippet: A z-stack was acquired every minute for 100 min total using a 60× oil-immersion objective (Nikon Plan Apo VC, Nature Cell Biology Article https://doi.org/10.1038/s41556-023-01096-x 1.4 numerical aperture).

    Software:

    Article Title: Deconwolf enables high-performance deconvolution of widefield fluorescence microscopy images
    Article Snippet: The nomenclature is the same as in ref. . CT, layer 6 corticothalamic neurons; IT, intratelencephalic neurons; NP, near-projecting neurons; OPC, oligodendrocyte precursor cells; PVALB, parvalbumin-expressing neurons; SST, somatostatin-expressing neurons; VIP, vasoactive intestinal peptide-expressing neurons. c , Maximum z-projection of a z-stack from the previously published ChrX-46plex OligoFISSEQ dataset , without deconvolution (Raw) or after deconvolution with DW or with the deconvolution module in the commercial software NIS Elements AR (Nikon) (NIS).

    Article Title: Metformin and Inhibition of Transforming Growth Factor-Beta Stimulate In Vitro Transport in Primary Renal Tubule Cells
    Article Snippet: Renal cells on transwell membranes were stained for NKCC2 and ZO-1 immunofluorescence was also imaged on a Nikon structured illumination microscope (SIM) as a Z-stack at 0.12-μm thickness using a × 100 total internal reflection fluorescence objective.

    Article Title: Endothelial Cell Selectivity to Nanoparticles Depends on Mechanical Phenotype
    Article Snippet: To confirm the endocytosis of the red dye-loaded (excitation/emission wavelengths: 580/605) carboxylatemodified polystyrene 100 nm NPs, fluorescence images of the cells were taken under a super-resolution microscope, Z-stack (Nikon).

    Article Title: Transcription bodies regulate gene expression by sequestering CDK9
    Article Snippet: Multiposition, z -stack (20 μm in 41 steps, NIDAQ Piezo Z) timelapse (2 min time interval) imaging was performed with a Nikon ×60/1.2 Plan Apochromat VC water objective.

    Article Title: Endogenous Extracellular Matrix Regulates the Response of Osteosarcoma 3D Spheroids to Doxorubicin.
    Article Snippet: Images were acquired with a 25× water-immersion objective and multi-photon excitation fluorescence, resonant scanning, zoom at 1, and line average of 4 for a total of 100 slices on the Z-stack (A1R MP confocal microscope, Nikon).

    Article Title: SARS-CoV-2 infection induces DNA damage, through CHK1 degradation and impaired 53BP1 recruitment, and cellular senescence
    Article Snippet: A z -stack was acquired every minute for 100 min total using a 60× oil-immersion objective (Nikon Plan Apo VC, 1.4 numerical aperture).

    Article Title: Host Retromer Protein Sorting Nexin 2 Interacts with Human Respiratory Syncytial Virus Structural Proteins and is Required for Efficient Viral Production
    Article Snippet: The cell nuclei staining was omitted. (E) HRSV infected and transfected with Vps4-GFP plasmid. (F) PLA for HRSV N and Vps4-GFP performed in HRSV-infected cells and transfected with Vps4-GFP plasmid. (G) A merge between panels E and F. (H) HRSV-infected cells stained for TGN46. (I) PLA performed in HRSV-infected cells without using the HRSV N primary antibody as a biological control of the experiment. (J) Merge between panels H and I. (K) TGN46 in HRSV-infected cells. (L) PLA for HRSV F and N proteins. (M) Merge of panels K and L. (N) Proximity/interaction of F and N occurs at the Golgi compartment; approximately 35% of the cells analyzed showed PLA positive staining as in panels L and M. The plot profile in panel N was performed following the arrow traced in panel M. Panels A to D represent a single plane from a Z-stack imaging from a Nikon N-SIM microscope (superresolution imaging), while E to M represent a single focal plane of two independent experiments taken with a Zeiss 780 confocal microscope.

    Article Title: SARS-CoV-2 infection induces DNA damage, through CHK1 degradation and impaired 53BP1 recruitment, and cellular senescence.
    Article Snippet: A z-stack was acquired every minute for 100 min total using a 60× oil-immersion objective (Nikon Plan Apo VC, Nature Cell Biology Article https://doi.org/10.1038/s41556-023-01096-x 1.4 numerical aperture).

    Staining:

    Article Title: Deconwolf enables high-performance deconvolution of widefield fluorescence microscopy images
    Article Snippet: The nomenclature is the same as in ref. . CT, layer 6 corticothalamic neurons; IT, intratelencephalic neurons; NP, near-projecting neurons; OPC, oligodendrocyte precursor cells; PVALB, parvalbumin-expressing neurons; SST, somatostatin-expressing neurons; VIP, vasoactive intestinal peptide-expressing neurons. c , Maximum z-projection of a z-stack from the previously published ChrX-46plex OligoFISSEQ dataset , without deconvolution (Raw) or after deconvolution with DW or with the deconvolution module in the commercial software NIS Elements AR (Nikon) (NIS).

    Article Title: Metformin and Inhibition of Transforming Growth Factor-Beta Stimulate In Vitro Transport in Primary Renal Tubule Cells
    Article Snippet: Renal cells on transwell membranes were stained for NKCC2 and ZO-1 immunofluorescence was also imaged on a Nikon structured illumination microscope (SIM) as a Z-stack at 0.12-μm thickness using a × 100 total internal reflection fluorescence objective.

    Article Title: Endothelial Cell Selectivity to Nanoparticles Depends on Mechanical Phenotype
    Article Snippet: To confirm the endocytosis of the red dye-loaded (excitation/emission wavelengths: 580/605) carboxylatemodified polystyrene 100 nm NPs, fluorescence images of the cells were taken under a super-resolution microscope, Z-stack (Nikon).

    Article Title: Transcription bodies regulate gene expression by sequestering CDK9
    Article Snippet: Multiposition, z -stack (20 μm in 41 steps, NIDAQ Piezo Z) timelapse (2 min time interval) imaging was performed with a Nikon ×60/1.2 Plan Apochromat VC water objective.

    Article Title: Endogenous Extracellular Matrix Regulates the Response of Osteosarcoma 3D Spheroids to Doxorubicin.
    Article Snippet: Images were acquired with a 25× water-immersion objective and multi-photon excitation fluorescence, resonant scanning, zoom at 1, and line average of 4 for a total of 100 slices on the Z-stack (A1R MP confocal microscope, Nikon).

    Article Title: SARS-CoV-2 infection induces DNA damage, through CHK1 degradation and impaired 53BP1 recruitment, and cellular senescence
    Article Snippet: A z -stack was acquired every minute for 100 min total using a 60× oil-immersion objective (Nikon Plan Apo VC, 1.4 numerical aperture).

    Article Title: Host Retromer Protein Sorting Nexin 2 Interacts with Human Respiratory Syncytial Virus Structural Proteins and is Required for Efficient Viral Production
    Article Snippet: The cell nuclei staining was omitted. (E) HRSV infected and transfected with Vps4-GFP plasmid. (F) PLA for HRSV N and Vps4-GFP performed in HRSV-infected cells and transfected with Vps4-GFP plasmid. (G) A merge between panels E and F. (H) HRSV-infected cells stained for TGN46. (I) PLA performed in HRSV-infected cells without using the HRSV N primary antibody as a biological control of the experiment. (J) Merge between panels H and I. (K) TGN46 in HRSV-infected cells. (L) PLA for HRSV F and N proteins. (M) Merge of panels K and L. (N) Proximity/interaction of F and N occurs at the Golgi compartment; approximately 35% of the cells analyzed showed PLA positive staining as in panels L and M. The plot profile in panel N was performed following the arrow traced in panel M. Panels A to D represent a single plane from a Z-stack imaging from a Nikon N-SIM microscope (superresolution imaging), while E to M represent a single focal plane of two independent experiments taken with a Zeiss 780 confocal microscope.

    Article Title: SARS-CoV-2 infection induces DNA damage, through CHK1 degradation and impaired 53BP1 recruitment, and cellular senescence.
    Article Snippet: A z-stack was acquired every minute for 100 min total using a 60× oil-immersion objective (Nikon Plan Apo VC, Nature Cell Biology Article https://doi.org/10.1038/s41556-023-01096-x 1.4 numerical aperture).

    Infection:

    Article Title: Deconwolf enables high-performance deconvolution of widefield fluorescence microscopy images
    Article Snippet: The nomenclature is the same as in ref. . CT, layer 6 corticothalamic neurons; IT, intratelencephalic neurons; NP, near-projecting neurons; OPC, oligodendrocyte precursor cells; PVALB, parvalbumin-expressing neurons; SST, somatostatin-expressing neurons; VIP, vasoactive intestinal peptide-expressing neurons. c , Maximum z-projection of a z-stack from the previously published ChrX-46plex OligoFISSEQ dataset , without deconvolution (Raw) or after deconvolution with DW or with the deconvolution module in the commercial software NIS Elements AR (Nikon) (NIS).

    Article Title: Metformin and Inhibition of Transforming Growth Factor-Beta Stimulate In Vitro Transport in Primary Renal Tubule Cells
    Article Snippet: Renal cells on transwell membranes were stained for NKCC2 and ZO-1 immunofluorescence was also imaged on a Nikon structured illumination microscope (SIM) as a Z-stack at 0.12-μm thickness using a × 100 total internal reflection fluorescence objective.

    Article Title: Endothelial Cell Selectivity to Nanoparticles Depends on Mechanical Phenotype
    Article Snippet: To confirm the endocytosis of the red dye-loaded (excitation/emission wavelengths: 580/605) carboxylatemodified polystyrene 100 nm NPs, fluorescence images of the cells were taken under a super-resolution microscope, Z-stack (Nikon).

    Article Title: Transcription bodies regulate gene expression by sequestering CDK9
    Article Snippet: Multiposition, z -stack (20 μm in 41 steps, NIDAQ Piezo Z) timelapse (2 min time interval) imaging was performed with a Nikon ×60/1.2 Plan Apochromat VC water objective.

    Article Title: Endogenous Extracellular Matrix Regulates the Response of Osteosarcoma 3D Spheroids to Doxorubicin.
    Article Snippet: Images were acquired with a 25× water-immersion objective and multi-photon excitation fluorescence, resonant scanning, zoom at 1, and line average of 4 for a total of 100 slices on the Z-stack (A1R MP confocal microscope, Nikon).

    Article Title: SARS-CoV-2 infection induces DNA damage, through CHK1 degradation and impaired 53BP1 recruitment, and cellular senescence
    Article Snippet: A z -stack was acquired every minute for 100 min total using a 60× oil-immersion objective (Nikon Plan Apo VC, 1.4 numerical aperture).

    Article Title: Host Retromer Protein Sorting Nexin 2 Interacts with Human Respiratory Syncytial Virus Structural Proteins and is Required for Efficient Viral Production
    Article Snippet: The cell nuclei staining was omitted. (E) HRSV infected and transfected with Vps4-GFP plasmid. (F) PLA for HRSV N and Vps4-GFP performed in HRSV-infected cells and transfected with Vps4-GFP plasmid. (G) A merge between panels E and F. (H) HRSV-infected cells stained for TGN46. (I) PLA performed in HRSV-infected cells without using the HRSV N primary antibody as a biological control of the experiment. (J) Merge between panels H and I. (K) TGN46 in HRSV-infected cells. (L) PLA for HRSV F and N proteins. (M) Merge of panels K and L. (N) Proximity/interaction of F and N occurs at the Golgi compartment; approximately 35% of the cells analyzed showed PLA positive staining as in panels L and M. The plot profile in panel N was performed following the arrow traced in panel M. Panels A to D represent a single plane from a Z-stack imaging from a Nikon N-SIM microscope (superresolution imaging), while E to M represent a single focal plane of two independent experiments taken with a Zeiss 780 confocal microscope.

    Article Title: SARS-CoV-2 infection induces DNA damage, through CHK1 degradation and impaired 53BP1 recruitment, and cellular senescence.
    Article Snippet: A z-stack was acquired every minute for 100 min total using a 60× oil-immersion objective (Nikon Plan Apo VC, Nature Cell Biology Article https://doi.org/10.1038/s41556-023-01096-x 1.4 numerical aperture).

    Transfection:

    Article Title: Deconwolf enables high-performance deconvolution of widefield fluorescence microscopy images
    Article Snippet: The nomenclature is the same as in ref. . CT, layer 6 corticothalamic neurons; IT, intratelencephalic neurons; NP, near-projecting neurons; OPC, oligodendrocyte precursor cells; PVALB, parvalbumin-expressing neurons; SST, somatostatin-expressing neurons; VIP, vasoactive intestinal peptide-expressing neurons. c , Maximum z-projection of a z-stack from the previously published ChrX-46plex OligoFISSEQ dataset , without deconvolution (Raw) or after deconvolution with DW or with the deconvolution module in the commercial software NIS Elements AR (Nikon) (NIS).

    Article Title: Metformin and Inhibition of Transforming Growth Factor-Beta Stimulate In Vitro Transport in Primary Renal Tubule Cells
    Article Snippet: Renal cells on transwell membranes were stained for NKCC2 and ZO-1 immunofluorescence was also imaged on a Nikon structured illumination microscope (SIM) as a Z-stack at 0.12-μm thickness using a × 100 total internal reflection fluorescence objective.

    Article Title: Endothelial Cell Selectivity to Nanoparticles Depends on Mechanical Phenotype
    Article Snippet: To confirm the endocytosis of the red dye-loaded (excitation/emission wavelengths: 580/605) carboxylatemodified polystyrene 100 nm NPs, fluorescence images of the cells were taken under a super-resolution microscope, Z-stack (Nikon).

    Article Title: Transcription bodies regulate gene expression by sequestering CDK9
    Article Snippet: Multiposition, z -stack (20 μm in 41 steps, NIDAQ Piezo Z) timelapse (2 min time interval) imaging was performed with a Nikon ×60/1.2 Plan Apochromat VC water objective.

    Article Title: Endogenous Extracellular Matrix Regulates the Response of Osteosarcoma 3D Spheroids to Doxorubicin.
    Article Snippet: Images were acquired with a 25× water-immersion objective and multi-photon excitation fluorescence, resonant scanning, zoom at 1, and line average of 4 for a total of 100 slices on the Z-stack (A1R MP confocal microscope, Nikon).

    Article Title: SARS-CoV-2 infection induces DNA damage, through CHK1 degradation and impaired 53BP1 recruitment, and cellular senescence
    Article Snippet: A z -stack was acquired every minute for 100 min total using a 60× oil-immersion objective (Nikon Plan Apo VC, 1.4 numerical aperture).

    Article Title: Host Retromer Protein Sorting Nexin 2 Interacts with Human Respiratory Syncytial Virus Structural Proteins and is Required for Efficient Viral Production
    Article Snippet: The cell nuclei staining was omitted. (E) HRSV infected and transfected with Vps4-GFP plasmid. (F) PLA for HRSV N and Vps4-GFP performed in HRSV-infected cells and transfected with Vps4-GFP plasmid. (G) A merge between panels E and F. (H) HRSV-infected cells stained for TGN46. (I) PLA performed in HRSV-infected cells without using the HRSV N primary antibody as a biological control of the experiment. (J) Merge between panels H and I. (K) TGN46 in HRSV-infected cells. (L) PLA for HRSV F and N proteins. (M) Merge of panels K and L. (N) Proximity/interaction of F and N occurs at the Golgi compartment; approximately 35% of the cells analyzed showed PLA positive staining as in panels L and M. The plot profile in panel N was performed following the arrow traced in panel M. Panels A to D represent a single plane from a Z-stack imaging from a Nikon N-SIM microscope (superresolution imaging), while E to M represent a single focal plane of two independent experiments taken with a Zeiss 780 confocal microscope.

    Article Title: SARS-CoV-2 infection induces DNA damage, through CHK1 degradation and impaired 53BP1 recruitment, and cellular senescence.
    Article Snippet: A z-stack was acquired every minute for 100 min total using a 60× oil-immersion objective (Nikon Plan Apo VC, Nature Cell Biology Article https://doi.org/10.1038/s41556-023-01096-x 1.4 numerical aperture).

    Plasmid Preparation:

    Article Title: Deconwolf enables high-performance deconvolution of widefield fluorescence microscopy images
    Article Snippet: The nomenclature is the same as in ref. . CT, layer 6 corticothalamic neurons; IT, intratelencephalic neurons; NP, near-projecting neurons; OPC, oligodendrocyte precursor cells; PVALB, parvalbumin-expressing neurons; SST, somatostatin-expressing neurons; VIP, vasoactive intestinal peptide-expressing neurons. c , Maximum z-projection of a z-stack from the previously published ChrX-46plex OligoFISSEQ dataset , without deconvolution (Raw) or after deconvolution with DW or with the deconvolution module in the commercial software NIS Elements AR (Nikon) (NIS).

    Article Title: Metformin and Inhibition of Transforming Growth Factor-Beta Stimulate In Vitro Transport in Primary Renal Tubule Cells
    Article Snippet: Renal cells on transwell membranes were stained for NKCC2 and ZO-1 immunofluorescence was also imaged on a Nikon structured illumination microscope (SIM) as a Z-stack at 0.12-μm thickness using a × 100 total internal reflection fluorescence objective.

    Article Title: Endothelial Cell Selectivity to Nanoparticles Depends on Mechanical Phenotype
    Article Snippet: To confirm the endocytosis of the red dye-loaded (excitation/emission wavelengths: 580/605) carboxylatemodified polystyrene 100 nm NPs, fluorescence images of the cells were taken under a super-resolution microscope, Z-stack (Nikon).

    Article Title: Transcription bodies regulate gene expression by sequestering CDK9
    Article Snippet: Multiposition, z -stack (20 μm in 41 steps, NIDAQ Piezo Z) timelapse (2 min time interval) imaging was performed with a Nikon ×60/1.2 Plan Apochromat VC water objective.

    Article Title: Endogenous Extracellular Matrix Regulates the Response of Osteosarcoma 3D Spheroids to Doxorubicin.
    Article Snippet: Images were acquired with a 25× water-immersion objective and multi-photon excitation fluorescence, resonant scanning, zoom at 1, and line average of 4 for a total of 100 slices on the Z-stack (A1R MP confocal microscope, Nikon).

    Article Title: SARS-CoV-2 infection induces DNA damage, through CHK1 degradation and impaired 53BP1 recruitment, and cellular senescence
    Article Snippet: A z -stack was acquired every minute for 100 min total using a 60× oil-immersion objective (Nikon Plan Apo VC, 1.4 numerical aperture).

    Article Title: Host Retromer Protein Sorting Nexin 2 Interacts with Human Respiratory Syncytial Virus Structural Proteins and is Required for Efficient Viral Production
    Article Snippet: The cell nuclei staining was omitted. (E) HRSV infected and transfected with Vps4-GFP plasmid. (F) PLA for HRSV N and Vps4-GFP performed in HRSV-infected cells and transfected with Vps4-GFP plasmid. (G) A merge between panels E and F. (H) HRSV-infected cells stained for TGN46. (I) PLA performed in HRSV-infected cells without using the HRSV N primary antibody as a biological control of the experiment. (J) Merge between panels H and I. (K) TGN46 in HRSV-infected cells. (L) PLA for HRSV F and N proteins. (M) Merge of panels K and L. (N) Proximity/interaction of F and N occurs at the Golgi compartment; approximately 35% of the cells analyzed showed PLA positive staining as in panels L and M. The plot profile in panel N was performed following the arrow traced in panel M. Panels A to D represent a single plane from a Z-stack imaging from a Nikon N-SIM microscope (superresolution imaging), while E to M represent a single focal plane of two independent experiments taken with a Zeiss 780 confocal microscope.

    Article Title: SARS-CoV-2 infection induces DNA damage, through CHK1 degradation and impaired 53BP1 recruitment, and cellular senescence.
    Article Snippet: A z-stack was acquired every minute for 100 min total using a 60× oil-immersion objective (Nikon Plan Apo VC, Nature Cell Biology Article https://doi.org/10.1038/s41556-023-01096-x 1.4 numerical aperture).

    Proximity Ligation Assay:

    Article Title: Deconwolf enables high-performance deconvolution of widefield fluorescence microscopy images
    Article Snippet: The nomenclature is the same as in ref. . CT, layer 6 corticothalamic neurons; IT, intratelencephalic neurons; NP, near-projecting neurons; OPC, oligodendrocyte precursor cells; PVALB, parvalbumin-expressing neurons; SST, somatostatin-expressing neurons; VIP, vasoactive intestinal peptide-expressing neurons. c , Maximum z-projection of a z-stack from the previously published ChrX-46plex OligoFISSEQ dataset , without deconvolution (Raw) or after deconvolution with DW or with the deconvolution module in the commercial software NIS Elements AR (Nikon) (NIS).

    Article Title: Metformin and Inhibition of Transforming Growth Factor-Beta Stimulate In Vitro Transport in Primary Renal Tubule Cells
    Article Snippet: Renal cells on transwell membranes were stained for NKCC2 and ZO-1 immunofluorescence was also imaged on a Nikon structured illumination microscope (SIM) as a Z-stack at 0.12-μm thickness using a × 100 total internal reflection fluorescence objective.

    Article Title: Endothelial Cell Selectivity to Nanoparticles Depends on Mechanical Phenotype
    Article Snippet: To confirm the endocytosis of the red dye-loaded (excitation/emission wavelengths: 580/605) carboxylatemodified polystyrene 100 nm NPs, fluorescence images of the cells were taken under a super-resolution microscope, Z-stack (Nikon).

    Article Title: Transcription bodies regulate gene expression by sequestering CDK9
    Article Snippet: Multiposition, z -stack (20 μm in 41 steps, NIDAQ Piezo Z) timelapse (2 min time interval) imaging was performed with a Nikon ×60/1.2 Plan Apochromat VC water objective.

    Article Title: Endogenous Extracellular Matrix Regulates the Response of Osteosarcoma 3D Spheroids to Doxorubicin.
    Article Snippet: Images were acquired with a 25× water-immersion objective and multi-photon excitation fluorescence, resonant scanning, zoom at 1, and line average of 4 for a total of 100 slices on the Z-stack (A1R MP confocal microscope, Nikon).

    Article Title: SARS-CoV-2 infection induces DNA damage, through CHK1 degradation and impaired 53BP1 recruitment, and cellular senescence
    Article Snippet: A z -stack was acquired every minute for 100 min total using a 60× oil-immersion objective (Nikon Plan Apo VC, 1.4 numerical aperture).

    Article Title: Host Retromer Protein Sorting Nexin 2 Interacts with Human Respiratory Syncytial Virus Structural Proteins and is Required for Efficient Viral Production
    Article Snippet: The cell nuclei staining was omitted. (E) HRSV infected and transfected with Vps4-GFP plasmid. (F) PLA for HRSV N and Vps4-GFP performed in HRSV-infected cells and transfected with Vps4-GFP plasmid. (G) A merge between panels E and F. (H) HRSV-infected cells stained for TGN46. (I) PLA performed in HRSV-infected cells without using the HRSV N primary antibody as a biological control of the experiment. (J) Merge between panels H and I. (K) TGN46 in HRSV-infected cells. (L) PLA for HRSV F and N proteins. (M) Merge of panels K and L. (N) Proximity/interaction of F and N occurs at the Golgi compartment; approximately 35% of the cells analyzed showed PLA positive staining as in panels L and M. The plot profile in panel N was performed following the arrow traced in panel M. Panels A to D represent a single plane from a Z-stack imaging from a Nikon N-SIM microscope (superresolution imaging), while E to M represent a single focal plane of two independent experiments taken with a Zeiss 780 confocal microscope.

    Article Title: SARS-CoV-2 infection induces DNA damage, through CHK1 degradation and impaired 53BP1 recruitment, and cellular senescence.
    Article Snippet: A z-stack was acquired every minute for 100 min total using a 60× oil-immersion objective (Nikon Plan Apo VC, Nature Cell Biology Article https://doi.org/10.1038/s41556-023-01096-x 1.4 numerical aperture).

    Control:

    Article Title: Deconwolf enables high-performance deconvolution of widefield fluorescence microscopy images
    Article Snippet: The nomenclature is the same as in ref. . CT, layer 6 corticothalamic neurons; IT, intratelencephalic neurons; NP, near-projecting neurons; OPC, oligodendrocyte precursor cells; PVALB, parvalbumin-expressing neurons; SST, somatostatin-expressing neurons; VIP, vasoactive intestinal peptide-expressing neurons. c , Maximum z-projection of a z-stack from the previously published ChrX-46plex OligoFISSEQ dataset , without deconvolution (Raw) or after deconvolution with DW or with the deconvolution module in the commercial software NIS Elements AR (Nikon) (NIS).

    Article Title: Metformin and Inhibition of Transforming Growth Factor-Beta Stimulate In Vitro Transport in Primary Renal Tubule Cells
    Article Snippet: Renal cells on transwell membranes were stained for NKCC2 and ZO-1 immunofluorescence was also imaged on a Nikon structured illumination microscope (SIM) as a Z-stack at 0.12-μm thickness using a × 100 total internal reflection fluorescence objective.

    Article Title: Endothelial Cell Selectivity to Nanoparticles Depends on Mechanical Phenotype
    Article Snippet: To confirm the endocytosis of the red dye-loaded (excitation/emission wavelengths: 580/605) carboxylatemodified polystyrene 100 nm NPs, fluorescence images of the cells were taken under a super-resolution microscope, Z-stack (Nikon).

    Article Title: Transcription bodies regulate gene expression by sequestering CDK9
    Article Snippet: Multiposition, z -stack (20 μm in 41 steps, NIDAQ Piezo Z) timelapse (2 min time interval) imaging was performed with a Nikon ×60/1.2 Plan Apochromat VC water objective.

    Article Title: Endogenous Extracellular Matrix Regulates the Response of Osteosarcoma 3D Spheroids to Doxorubicin.
    Article Snippet: Images were acquired with a 25× water-immersion objective and multi-photon excitation fluorescence, resonant scanning, zoom at 1, and line average of 4 for a total of 100 slices on the Z-stack (A1R MP confocal microscope, Nikon).

    Article Title: SARS-CoV-2 infection induces DNA damage, through CHK1 degradation and impaired 53BP1 recruitment, and cellular senescence
    Article Snippet: A z -stack was acquired every minute for 100 min total using a 60× oil-immersion objective (Nikon Plan Apo VC, 1.4 numerical aperture).

    Article Title: Host Retromer Protein Sorting Nexin 2 Interacts with Human Respiratory Syncytial Virus Structural Proteins and is Required for Efficient Viral Production
    Article Snippet: The cell nuclei staining was omitted. (E) HRSV infected and transfected with Vps4-GFP plasmid. (F) PLA for HRSV N and Vps4-GFP performed in HRSV-infected cells and transfected with Vps4-GFP plasmid. (G) A merge between panels E and F. (H) HRSV-infected cells stained for TGN46. (I) PLA performed in HRSV-infected cells without using the HRSV N primary antibody as a biological control of the experiment. (J) Merge between panels H and I. (K) TGN46 in HRSV-infected cells. (L) PLA for HRSV F and N proteins. (M) Merge of panels K and L. (N) Proximity/interaction of F and N occurs at the Golgi compartment; approximately 35% of the cells analyzed showed PLA positive staining as in panels L and M. The plot profile in panel N was performed following the arrow traced in panel M. Panels A to D represent a single plane from a Z-stack imaging from a Nikon N-SIM microscope (superresolution imaging), while E to M represent a single focal plane of two independent experiments taken with a Zeiss 780 confocal microscope.

    Article Title: SARS-CoV-2 infection induces DNA damage, through CHK1 degradation and impaired 53BP1 recruitment, and cellular senescence.
    Article Snippet: A z-stack was acquired every minute for 100 min total using a 60× oil-immersion objective (Nikon Plan Apo VC, Nature Cell Biology Article https://doi.org/10.1038/s41556-023-01096-x 1.4 numerical aperture).

    Imaging:

    Article Title: Deconwolf enables high-performance deconvolution of widefield fluorescence microscopy images
    Article Snippet: The nomenclature is the same as in ref. . CT, layer 6 corticothalamic neurons; IT, intratelencephalic neurons; NP, near-projecting neurons; OPC, oligodendrocyte precursor cells; PVALB, parvalbumin-expressing neurons; SST, somatostatin-expressing neurons; VIP, vasoactive intestinal peptide-expressing neurons. c , Maximum z-projection of a z-stack from the previously published ChrX-46plex OligoFISSEQ dataset , without deconvolution (Raw) or after deconvolution with DW or with the deconvolution module in the commercial software NIS Elements AR (Nikon) (NIS).

    Article Title: Metformin and Inhibition of Transforming Growth Factor-Beta Stimulate In Vitro Transport in Primary Renal Tubule Cells
    Article Snippet: Renal cells on transwell membranes were stained for NKCC2 and ZO-1 immunofluorescence was also imaged on a Nikon structured illumination microscope (SIM) as a Z-stack at 0.12-μm thickness using a × 100 total internal reflection fluorescence objective.

    Article Title: Endothelial Cell Selectivity to Nanoparticles Depends on Mechanical Phenotype
    Article Snippet: To confirm the endocytosis of the red dye-loaded (excitation/emission wavelengths: 580/605) carboxylatemodified polystyrene 100 nm NPs, fluorescence images of the cells were taken under a super-resolution microscope, Z-stack (Nikon).

    Article Title: Transcription bodies regulate gene expression by sequestering CDK9
    Article Snippet: Multiposition, z -stack (20 μm in 41 steps, NIDAQ Piezo Z) timelapse (2 min time interval) imaging was performed with a Nikon ×60/1.2 Plan Apochromat VC water objective.

    Article Title: Endogenous Extracellular Matrix Regulates the Response of Osteosarcoma 3D Spheroids to Doxorubicin.
    Article Snippet: Images were acquired with a 25× water-immersion objective and multi-photon excitation fluorescence, resonant scanning, zoom at 1, and line average of 4 for a total of 100 slices on the Z-stack (A1R MP confocal microscope, Nikon).

    Article Title: SARS-CoV-2 infection induces DNA damage, through CHK1 degradation and impaired 53BP1 recruitment, and cellular senescence
    Article Snippet: A z -stack was acquired every minute for 100 min total using a 60× oil-immersion objective (Nikon Plan Apo VC, 1.4 numerical aperture).

    Article Title: Host Retromer Protein Sorting Nexin 2 Interacts with Human Respiratory Syncytial Virus Structural Proteins and is Required for Efficient Viral Production
    Article Snippet: The cell nuclei staining was omitted. (E) HRSV infected and transfected with Vps4-GFP plasmid. (F) PLA for HRSV N and Vps4-GFP performed in HRSV-infected cells and transfected with Vps4-GFP plasmid. (G) A merge between panels E and F. (H) HRSV-infected cells stained for TGN46. (I) PLA performed in HRSV-infected cells without using the HRSV N primary antibody as a biological control of the experiment. (J) Merge between panels H and I. (K) TGN46 in HRSV-infected cells. (L) PLA for HRSV F and N proteins. (M) Merge of panels K and L. (N) Proximity/interaction of F and N occurs at the Golgi compartment; approximately 35% of the cells analyzed showed PLA positive staining as in panels L and M. The plot profile in panel N was performed following the arrow traced in panel M. Panels A to D represent a single plane from a Z-stack imaging from a Nikon N-SIM microscope (superresolution imaging), while E to M represent a single focal plane of two independent experiments taken with a Zeiss 780 confocal microscope.

    Article Title: SARS-CoV-2 infection induces DNA damage, through CHK1 degradation and impaired 53BP1 recruitment, and cellular senescence.
    Article Snippet: A z-stack was acquired every minute for 100 min total using a 60× oil-immersion objective (Nikon Plan Apo VC, Nature Cell Biology Article https://doi.org/10.1038/s41556-023-01096-x 1.4 numerical aperture).

    Immunofluorescence:

    Article Title: Deconwolf enables high-performance deconvolution of widefield fluorescence microscopy images
    Article Snippet: The nomenclature is the same as in ref. . CT, layer 6 corticothalamic neurons; IT, intratelencephalic neurons; NP, near-projecting neurons; OPC, oligodendrocyte precursor cells; PVALB, parvalbumin-expressing neurons; SST, somatostatin-expressing neurons; VIP, vasoactive intestinal peptide-expressing neurons. c , Maximum z-projection of a z-stack from the previously published ChrX-46plex OligoFISSEQ dataset , without deconvolution (Raw) or after deconvolution with DW or with the deconvolution module in the commercial software NIS Elements AR (Nikon) (NIS).

    Article Title: Metformin and Inhibition of Transforming Growth Factor-Beta Stimulate In Vitro Transport in Primary Renal Tubule Cells
    Article Snippet: Renal cells on transwell membranes were stained for NKCC2 and ZO-1 immunofluorescence was also imaged on a Nikon structured illumination microscope (SIM) as a Z-stack at 0.12-μm thickness using a × 100 total internal reflection fluorescence objective.

    Article Title: Endothelial Cell Selectivity to Nanoparticles Depends on Mechanical Phenotype
    Article Snippet: To confirm the endocytosis of the red dye-loaded (excitation/emission wavelengths: 580/605) carboxylatemodified polystyrene 100 nm NPs, fluorescence images of the cells were taken under a super-resolution microscope, Z-stack (Nikon).

    Article Title: Transcription bodies regulate gene expression by sequestering CDK9
    Article Snippet: Multiposition, z -stack (20 μm in 41 steps, NIDAQ Piezo Z) timelapse (2 min time interval) imaging was performed with a Nikon ×60/1.2 Plan Apochromat VC water objective.

    Article Title: Endogenous Extracellular Matrix Regulates the Response of Osteosarcoma 3D Spheroids to Doxorubicin.
    Article Snippet: Images were acquired with a 25× water-immersion objective and multi-photon excitation fluorescence, resonant scanning, zoom at 1, and line average of 4 for a total of 100 slices on the Z-stack (A1R MP confocal microscope, Nikon).

    Article Title: SARS-CoV-2 infection induces DNA damage, through CHK1 degradation and impaired 53BP1 recruitment, and cellular senescence
    Article Snippet: A z -stack was acquired every minute for 100 min total using a 60× oil-immersion objective (Nikon Plan Apo VC, 1.4 numerical aperture).

    Article Title: Host Retromer Protein Sorting Nexin 2 Interacts with Human Respiratory Syncytial Virus Structural Proteins and is Required for Efficient Viral Production
    Article Snippet: The cell nuclei staining was omitted. (E) HRSV infected and transfected with Vps4-GFP plasmid. (F) PLA for HRSV N and Vps4-GFP performed in HRSV-infected cells and transfected with Vps4-GFP plasmid. (G) A merge between panels E and F. (H) HRSV-infected cells stained for TGN46. (I) PLA performed in HRSV-infected cells without using the HRSV N primary antibody as a biological control of the experiment. (J) Merge between panels H and I. (K) TGN46 in HRSV-infected cells. (L) PLA for HRSV F and N proteins. (M) Merge of panels K and L. (N) Proximity/interaction of F and N occurs at the Golgi compartment; approximately 35% of the cells analyzed showed PLA positive staining as in panels L and M. The plot profile in panel N was performed following the arrow traced in panel M. Panels A to D represent a single plane from a Z-stack imaging from a Nikon N-SIM microscope (superresolution imaging), while E to M represent a single focal plane of two independent experiments taken with a Zeiss 780 confocal microscope.

    Article Title: SARS-CoV-2 infection induces DNA damage, through CHK1 degradation and impaired 53BP1 recruitment, and cellular senescence.
    Article Snippet: A z-stack was acquired every minute for 100 min total using a 60× oil-immersion objective (Nikon Plan Apo VC, Nature Cell Biology Article https://doi.org/10.1038/s41556-023-01096-x 1.4 numerical aperture).



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