cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0pr7tq7
title: CIL:13408, Mus musculus, fibroblast. In Cell Image Library

description: Preparation: formaldehyde fixed tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image; photomultiplier tube (PMT)
Imaging mode: single-spot confocal microscopy; fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein; differences in adsorption or binding of stain
Visualization methods: primary antibody plus labeled secondary antibody; 4',6-diamidino-2-phenylindole (DAPI); Alexa Fluor 546
Processing history: linear methods
Data qualification: Processed;spatialmeasurements;intensitiesquantitation
description: Phosphorylated H2AX occurs preferentially in open chromatin. Wildtype mouse embryo fibroblasts were treated with the radiomimetic drug neocarzinostatin (NCS) for 1hour prior to being fixed and immunolabeled against the phosphorylated form of histone H2AX and co-stained with DAPI. MEFs were grown on glass coverslips and treated with 10 ng/ml NCS for 1 h or with 1 μM TSA for 8 h and were treated with 10 ng/ml NCS for an additional hour before being fixed in 2% freshly prepared PFA in PBS for 5 min at room temperature. Cells were immunolabeled using monoclonal antiphospho-H2AX antibody (clone JBW301; 1:1,000; Upstate Biotechnology) and goat anti–mouse AlexaFluor546 secondary antibody (Invitrogen). The cells were labeled for 30 min in PBS containing 100 nM DAPI, rinsed with PBS, and mounted on glass microscope slides in glycerol-based mounting media containing N-propyl gallate antifade (Sigma-Aldrich). A stack of confocal optical slices was captured through the depth of the nucleus (Z-axis) using a 63x Plan-Apochromat (N.A. 1.4) objective lens, an optical slice thickness of 800nm, a Z-step size of 200nm, and X-Y pixel size of 70nm. Individual optical slices were background subtracted and contrast adjusted only by stretching the histogram in a linear manner consistently for the different fluorescence channels. Image corresponds to Fig 6B, left panel in Kim et al. J Cell Biol. 178: 209-218. 2007.
DOI: 10.6075/j0tb15n9
title: CIL:13433, Homo sapiens, breast. In Cell Image Library

description: Preparation: formaldehyde fixed tissue; tissue in paraffin embedment
Relation to intact cell: microtome-sectioned tissue
Item type: charge coupled device (CCD)
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: differences in adsorption or binding of stain
Visualization methods: Rhodamine; Fluorescein (FITC); 4',6-diamidino-2-phenylindole (DAPI)
Processing history: 3D-deconvolution
Data qualification: Processed;spatialmeasurements
description: FISH detection of FOLS2 (FRA2; fluorescein, green) and CSF1R (rhodamine, red) in cancerous breast tissue. Nuclei counterstained with DAPI (blue). Tissue was fixed in formaldehyde, embedded in paraffin, and 4-5 micron sections cut. Stained sections were viewed using an Olympus IX70 microscope with a 60x 1.4 NA objective lens, and images acquired with a Photometrics CoolSnap CCD with a 1024X1024 pixel resolution, with a pixel size equivalent to 0.07427 microns in X and Y. Z-stacks were acquired to cover the thickness of the tissue section with a step size of 0.5 microns in the Z-direction, and subjected to deconvolution using SoftWoRx 3.5.1 software. A maximum intensity projection of this stack is included in this image group,
Part of this field of view is shown as a projection image in Fig 1A of Meaburn et al., 2009, J Cell Biol 187:801-812.
DOI: 10.6075/j07s7mpm
title: CIL:36491, Xenopus laevis, fertilized egg. In Cell Image Library

description: Images collected on a Zeiss LSM 710 confocal with a 10X 0.3 NA objective using 561 and 633 laser lines.
description: This image is part of a large data set of Xenopus laevis eggs imaged at various times post fertilization (the first number of the file name corresponds minutes, eg 30_2 is 30 min post fertilization). The embryos are stained for alpha-tubulin (green) using a directly labeled B-5-1-2 antibody and DNA (red).
description: Preparation: methanol fixed tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: single-spot confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope; distribution of a specific protein
Visualization methods: labeled primary antibody
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
DOI: 10.6075/j0d50kpw
title: CIL:13447, Saccharomyces cerevisiae S288c. In Cell Image Library

description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: EGFP
Processing history: constrained iterative deconvolution
Data qualification: Processed;spatialmeasurements;intensitiesquantitation
description: Intracellular localization of GFP-GOLPH3 in S. cerevisiae frq1-1 temperature-conditional strain grown at permissive temperature of 26C (control for 37C temperature-shift). In frq1-1 mutant after a 30 minute incubation at the restrictive temperature of 37C, GFP-GOLPH3 loses punctate localization and is mostly in the cytosol.The Golgi-localized PtdIns 4-kinase in yeast is composed of the Pik1 catalytic subunit and a myristoylated calcium-binding protein, Frq1. Vps74 is essential to maintain glycosyltransferases in the Golgi and results in this study reveal a previously unrecognized PtdIns4P-binding site in Vps74/GOLPH3 family proteins and link Pik1 signaling to retention of Golgi-resident proteins. Cells grown in liquid medium were mounted in growth medium and 3D image stacks were collected at 0.4-µm z increments on a DeltaVision workstation (Applied Precision) based on an inverted microscope (IX-70; Olympus) using a 100× NA 1.4 oil immersion lens. Images were captured at 23C with a 12-bit CCD camera (CoolSnap HQ; Photometrics) and deconvolved using the iterative-constrained algorithm (Agard, 1984) and the measured point spread function. One image from the approximate center of z stack is shown in Fig1A GOLPH3/frq1-1 26C panel in J Cell Biol. 187: 967-975. 2009. Images in Fig 1A include CIL#s 13439, 13440, 13441, 13442, 13443, 13444, 13445, 13446, 13447, 13448, 13458, 13459.
DOI: 10.6075/j0g44p0z
title: CIL:13446, Saccharomyces cerevisiae S288c. In Cell Image Library

description: Intracellular localization of GFP-GOLPH3 in S. cerevisiae pik1-83 temperature-conditional strain grown at restrictive temperature of 37C. In pik1-83 mutant after a 30 minute incubation at the restrictive temperature, GFP-GOLPH3 loses punctate localization and is mostly in the cytosol. The Golgi-localized PtdIns 4-kinase in yeast is composed of the Pik1 catalytic subunit and a myristoylated calcium-binding protein, Frq1. Vps74 is essential to maintain glycosyltransferases in the Golgi and results in this study reveal a previously unrecognized PtdIns4P-binding site in Vps74/GOLPH3 family proteins and link Pik1 signaling to retention of Golgi-resident proteins. Cells grown in liquid medium were mounted in growth medium and 3D image stacks were collected at 0.4-µm z increments on a DeltaVision workstation (Applied Precision) based on an inverted microscope (IX-70; Olympus) using a 100× NA 1.4 oil immersion lens. Images were captured at 23C with a 12-bit CCD camera (CoolSnap HQ; Photometrics) and deconvolved using the iterative-constrained algorithm (Agard, 1984) and the measured point spread function. One image from the approximate center of z stack is shown in Fig1A GOLPH3/pik1-83 37C panel in J Cell Biol. 187: 967-975. 2009. Images in Fig 1A include CIL#s 13439, 13440, 13441, 13442, 13443, 13444, 13445, 13446, 13447, 13448, 13458, 13459.
description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: EGFP
Processing history: constrained iterative deconvolution
Data qualification: Processed;spatialmeasurements;intensitiesquantitation
DOI: 10.6075/j0bk1b1c
title: CIL:13443, Saccharomyces cerevisiae S288c. In Cell Image Library

description: Intracellular localization of GFP-GOLPH3 in a wild-type S. cerevisiae background grown at 26C. In wild-type cells incubated at 26C or 37C, GFP-GOLPH localizes to intracellular membranes more robustly than yeast GFP-Vps74 with lower cytosolic GFP signal and brighter Golgi puncta compared with GFP-Vps74–expressing cells. The Golgi-localized PtdIns 4-kinase in yeast is composed of the Pik1 catalytic subunit and a myristoylated calcium-binding protein, Frq1. Vps74 is essential to maintain glycosyltransferases in the Golgi and results in this study reveal a previously unrecognized PtdIns4P-binding site in Vps74/GOLPH3 family proteins and link Pik1 signaling to retention of Golgi-resident proteins. Cells grown in liquid medium were mounted in growth medium and 3D image stacks were collected at 0.4-µm z increments on a DeltaVision workstation (Applied Precision) based on an inverted microscope (IX-70; Olympus) using a 100× NA 1.4 oil immersion lens. Images were captured at 23C with a 12-bit CCD camera (CoolSnap HQ; Photometrics) and deconvolved using the iterative-constrained algorithm (Agard, 1984) and the measured point spread function. One image from the approximate center of z stack is shown in Fig1A GOLPH3/wild-type 26C panel in J Cell Biol. 187: 967-975. 2009. Images in Fig 1A include CIL#s 13439, 13440, 13441, 13442, 13443, 13444, 13445, 13446, 13447, 13448, 13458, 13459.
description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: EGFP
Processing history: constrained iterative deconvolution
Data qualification: Processed;spatialmeasurements;intensitiesquantitation
DOI: 10.6075/j0ft8jsq
title: CIL:13442, Saccharomyces cerevisiae S288c. In Cell Image Library

description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: EGFP
Processing history: constrained iterative deconvolution
Data qualification: Processed;spatialmeasurements;intensitiesquantitation
description: Intracellular localization of GFP-Vps74 in S. cerevisiae frq1-1 temperature-conditional strain grown at restrictive temperature of 37C. In frq1-1 mutant after a 30 minute incubation at the restrictive temperature of 37C, GFP-Vps74 loses punctate localization and is mostly in the cytosol and nucleus. The Golgi-localized PtdIns 4-kinase in yeast is composed of the Pik1 catalytic subunit and a myristoylated calcium-binding protein, Frq1. Vps74 is essential to maintain glycosyltransferases in the Golgi and results in this study reveal a previously unrecognized PtdIns4P-binding site in Vps74/GOLPH3 family proteins and link Pik1 signaling to retention of Golgi-resident proteins. Cells grown in liquid medium were mounted in growth medium and 3D image stacks were collected at 0.4-µm z increments on a DeltaVision workstation (Applied Precision) based on an inverted microscope (IX-70; Olympus) using a 100× NA 1.4 oil immersion lens. Images were captured at 23C with a 12-bit CCD camera (CoolSnap HQ; Photometrics) and deconvolved using the iterative-constrained algorithm (Agard, 1984) and the measured point spread function. One image from the approximate center of z stack is shown in Fig1A Vps74/frq1-1 37C panel in J Cell Biol. 187: 967-975. 2009. Images in Fig 1A include CIL#s 13439, 13440, 13441, 13442, 13443, 13444, 13445, 13446, 13447, 13448, 13458, 13459.
DOI: 10.6075/j0df6pzr
title: CIL:13441, Saccharomyces cerevisiae S288c. In Cell Image Library

description: Intracellular localization of GFP-Vps74 in S. cerevisiae frq1-1 temperature-conditional strain grown at permissive temperature of 26C (control for 37C temperature-shift). In frq1-1 mutant after a 30 minute incubation at the restrictive temperature of 37C, GFP-Vps74 loses punctate localization and is mostly in the cytosol and nucleus. The Golgi-localized PtdIns 4-kinase in yeast is composed of the Pik1 catalytic subunit and a myristoylated calcium-binding protein, Frq1. Vps74 is essential to maintain glycosyltransferases in the Golgi and results in this study reveal a previously unrecognized PtdIns4P-binding site in Vps74/GOLPH3 family proteins and link Pik1 signaling to retention of Golgi-resident proteins. Cells grown in liquid medium were mounted in growth medium and 3D image stacks were collected at 0.4-µm z increments on a DeltaVision workstation (Applied Precision) based on an inverted microscope (IX-70; Olympus) using a 100× NA 1.4 oil immersion lens. Images were captured at 23C with a 12-bit CCD camera (CoolSnap HQ; Photometrics) and deconvolved using the iterative-constrained algorithm (Agard, 1984) and the measured point spread function. One image from the approximate center of z stack is shown in Fig1A Vps74/frq1-1 26C panel in J Cell Biol. 187: 967-975. 2009. Images in Fig 1A include CIL#s 13439, 13440, 13441, 13442, 13443, 13444, 13445, 13446, 13447, 13448, 13458, 13459.
description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: EGFP
Processing history: constrained iterative deconvolution
Data qualification: Processed;spatialmeasurements;intensitiesquantitation
DOI: 10.6075/j0dr2t81
title: CIL:13445, Saccharomyces cerevisiae S288c. In Cell Image Library

description: Intracellular localization of GFP-GOLPH3 in S. cerevisiae pik1-83 temperature-conditional strain grown at permissive temperature of 26C (control for 37C temperature-shift). In pik1-83 mutant after a 30 minute incubation at the restrictive temperature of 37C, GFP-GOLPH3 loses punctate localization and is mostly in the cytosol. The Golgi-localized PtdIns 4-kinase in yeast is composed of the Pik1 catalytic subunit and a myristoylated calcium-binding protein, Frq1. Vps74 is essential to maintain glycosyltransferases in the Golgi and results in this study reveal a previously unrecognized PtdIns4P-binding site in Vps74/GOLPH3 family proteins and link Pik1 signaling to retention of Golgi-resident proteins. Cells grown in liquid medium were mounted in growth medium and 3D image stacks were collected at 0.4-µm z increments on a DeltaVision workstation (Applied Precision) based on an inverted microscope (IX-70; Olympus) using a 100× NA 1.4 oil immersion lens. Images were captured at 23C with a 12-bit CCD camera (CoolSnap HQ; Photometrics) and deconvolved using the iterative-constrained algorithm (Agard, 1984) and the measured point spread function. One image from the approximate center of z stack is shown in Fig1A GOLPH3/pik1-83 26C panel in J Cell Biol. 187: 967-975. 2009. Images in Fig 1A include CIL#s 13439, 13440, 13441, 13442, 13443, 13444, 13445, 13446, 13447, 13448, 13458, 13459.
description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: EGFP
Processing history: constrained iterative deconvolution
Data qualification: Processed;spatialmeasurements;intensitiesquantitation
DOI: 10.6075/j0h70dh6
title: CIL:13444, Saccharomyces cerevisiae S288c. In Cell Image Library

description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: EGFP
Processing history: constrained iterative deconvolution
Data qualification: Processed;spatialmeasurements;intensitiesquantitation
description: Intracellular localization of GFP-GOLPH3 in a wild-type S. cerevisiae background grown at 37C. In wild-type cells incubated at 26C or 37C, GFP-GOLPH localizes to intracellular membranes more robustly than yeast GFP-Vps74 with lower cytosolic GFP signal and brighter Golgi puncta compared with GFP-Vps74–expressing cells. The Golgi-localized PtdIns 4-kinase in yeast is composed of the Pik1 catalytic subunit and a myristoylated calcium-binding protein, Frq1. Vps74 is essential to maintain glycosyltransferases in the Golgi and results in this study reveal a previously unrecognized PtdIns4P-binding site in Vps74/GOLPH3 family proteins and link Pik1 signaling to retention of Golgi-resident proteins. Cells grown in liquid medium were mounted in growth medium and 3D image stacks were collected at 0.4-µm z increments on a DeltaVision workstation (Applied Precision) based on an inverted microscope (IX-70; Olympus) using a 100× NA 1.4 oil immersion lens. Images were captured at 23C with a 12-bit CCD camera (CoolSnap HQ; Photometrics) and deconvolved using the iterative-constrained algorithm (Agard, 1984) and the measured point spread function. One image from the approximate center of z stack is shown in Fig1A GOLPH3/wild-type 37C panel in J Cell Biol. 187: 967-975. 2009. Images in Fig 1A include CIL#s 13439, 13440, 13441, 13442, 13443, 13444, 13445, 13446, 13447, 13448, 13458, 13459.
DOI: 10.6075/j0zk5grj
title: CIL:6166, Rattus, multipolar neuron. In Cell Image Library

description: Preparation: formaldehyde fixed tissue; detergent permeabilized
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope
Visualization methods: primary antibody plus labeled secondary antibody
Processing history: unprocessed raw data
Data qualification: Raw
description: Synapse formation in cultured hippocampal neurons after 7 days in vitro. Cells were immunostained for MAP2, a microtubule associated protein localized to dendrites but not axons (green), and synapsin I, a presynaptic vesicle protein (red) to reveal the development of presynaptic contacts along the dendritic arbor.
description: Embryonic rat hippocampal neurons were prepared as previously described (see Kaech and Banker, 2006, Nat Protoc). Cells were prepared for fluorescent staining as previously described (Withers and Banker, 1998, in Culturing Nerve Cells, MIT Press). Briefly, cells were fixed (4% formaldehyde, 4% sucrose in phosphate buffered saline, pH 7.4), permeabilized with 0.25% Triton and immunostained MAP2 (HM2, from Sigma with d549 conjugated secondary, excitation, 555, emission, 568, Jackson Immunoresearch). Images were acquired with a Leica DMRA microscope with a 16X PL Fluotar (0.5 NA) lens, Photometrics CoolSnap ES CCD camera and MetaMorph software. This merged image was generated using the color combine function in Metamorph.
DOI: 10.6075/j0m0443j
title: CIL:13437, Homo sapiens, breast. In Cell Image Library

description: FISH detection of ERBB2 (fluorescein, green) and MYC (rhodamine, red) in cancerous breast tissue. Nuclei counterstained with DAPI (blue). Tissue was fixed in formaldehyde, embedded in paraffin, and 4-5 micron sections cut. Stained sections were viewed using an Olympus IX70 microscope with a 60x 1.4 NA objective lens, and images acquired with a Photometrics CoolSnap CCD with a 1024X1024 pixel resolution, with a pixel size equivalent to 0.07427 microns in X and Y. Z-stacks were acquired to cover the thickness of the tissue section with a step size of 0.5 microns in the Z-direction, and subjected to deconvolution using SoftWoRx 3.5.1 software. A projected image of the stack is included in this image group.
Part of this field of view is shown in Fig 1B of Meaburn et al., 2009, J Cell Biol 187:801-812.
description: Preparation: formaldehyde fixed tissue; tissue in paraffin embedment
Relation to intact cell: microtome-sectioned tissue
Item type: charge coupled device (CCD)
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: differences in adsorption or binding of stain
Visualization methods: Rhodamine; Fluorescein (FITC); 4',6-diamidino-2-phenylindole (DAPI)
Processing history: 3D-deconvolution
Data qualification: Processed;spatialmeasurements
DOI: 10.6075/j0bv7fc4
title: CIL:13436, Homo sapiens, breast. In Cell Image Library

description: FISH detection of ERBB2 (florescein, green) and MYC (rhodamine, red) in normal breast tissue. Nuclei counterstained with DAPI (blue). Tissue was fixed in formaldehyde, embedded in paraffin, and 4-5 micron sections cut. Stained sections were viewed using an Olympus IX70 microscope with a 60x 1.4 NA objective lens, and images acquired with a Photometrics CoolSnap CCD with a 1024X1024 pixel resolution, with a pixel size equivalent to 0.07427 microns in X and Y. Shown is a maximum intensity projection of the stack. The complete stack is included in this group of images
 Part of this field of view is shown in Fig 1B of Meaburn et al., 2009, J Cell Biol 187:801-812.
description: Preparation: formaldehyde fixed tissue; tissue in paraffin embedment
Relation to intact cell: microtome-sectioned tissue
Item type: charge coupled device (CCD)
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: differences in adsorption or binding of stain
Visualization methods: Rhodamine; Fluorescein (FITC); 4',6-diamidino-2-phenylindole (DAPI)
Processing history: 3D-deconvolution
Data qualification: Processed;spatialmeasurements