cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0z89cfp
title: CIL:10116, 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; differences in adsorption or binding of stain
Visualization methods: phalloidin; primary antibody plus labeled secondary antibody
Processing history: unprocessed raw data
description: This multi-layer image shows the spatial relationship between filamentous actin (red) and microtubule array (green) in cultured hippocampal neurons, grown for 5 days in vitro. Actin staining (with rhodamine phalloidin) highlights the growing tips and filopodial extensions along axons and dendrites, while microtubule staining reveals the stable shafts of these processes. Some nonneuronal cells may also appear in the field.
Detailed Methods: 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, 37°C, 15 minutes), permeabilized (0.25% Triton, 7 minutes) and immunostained for tubulin (monoclonal DM1A, Sigma, with Alexa 488 conjugated secondary, Molecular Probes, excitation, 494, emission, 519) and rhodamine-conjugated phalloidin (Molecular Probes, excitation, 540, emission, 565). Fluorescent and phase images were acquired with a Leica DMRA microscope with a mercury arc lamp, a 20X lens (HC PL Fluotar, NA 0.5), Leica GFP filter set (excitation, BP 470/40; dichromatic mirror, 500, suppression filter, BP 525/50); Leica N3 filter set (excitation, BP546/12; dichromatic mirror, 565, suppression filter, BP 600/40), Photometrics CoolSnap ES CCD camera and MetaMorph software.
DOI: 10.6075/j06t0k86
title: CIL:34913. In Cell Image Library

description: Localization of Arp2/3 complex at actin filament branching points. Xenopus keratocytes and fibroblasts were treated with CD (0.2 μM for 30 min or 0.5 μM for 10 min), extracted in the presence of phalloidin, fixed with glutaraldehyde, treated with 33% methanol, and immunostained with p21 antibody followed by 10-nm gold-conjugated secondary antibody. Image corresponds to a single panel from Figure 4 in J Cell Biol. 1999 May 31;145(5):1009-26. All of the panels from Figure 4 are available as CIL:34902-34921.
description: Procedures for detergent extraction, immunostaining, S1 decoration, light, and EM were described previously (Svitkina et al., 1995, 1996, 1997;Verkhovsky et al., 1995; Svitkina and Borisy, 1998).
description: Preparation: permeabilized tissue; glutaraldehyde fixed tissue; methanol fixed tissue; phalloidin
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: optical path length gradient
Source of contrast: differences in deposition of metal shadow
Visualization methods: shadowing and plating; primary antibody plus labeled secondary antibody; platinum replica; immuno-gold
Processing history: unprocessed raw data
DOI: 10.6075/j0fq9vt7
title: CIL:716, Necturus maculosus, nucleate erythrocyte. In Cell Image Library

description: Preparation: unembedded tissue; glutaraldehyde fixed tissue
Relation to intact cell: isolated subcellular component
Item type: transmission electron microscopy (TEM)
Imaging mode: illumination by electrons; detection of electrons
Parameter imaged: electron density
Source of contrast: elastic scattering
Visualization methods: other negative stain
Processing history: raw unprocessed data
description: X-ray analysis shows that the nucleated erythrocytes of the amphibian Necturus maculosus (Mud Puppy) contains more ordered chromatin than most nuclei. Here, chromatin fibers were isolated from N. maculosus erythrocyte nuclei using mild micrococcal nuclease digestion, fixed briefly with glutaraldehyde, applied to thin carbon films and negatively stained with methylamine tungstate. ~30 nm fibers are seen, some exhibiting short regions with apparent structural order.
DOI: 10.6075/j03t9gzd
title: CIL: 54197, Homo sapiens, HeLa. In Cell Image Library

description: Kinome Atlas documented representative images for 456 kinases expressed in HeLa cells, and visualized by immunofluorescence staining of the epitope tag. Nuclei were stained with DAPI. Two representative views from confocal microscopy were collected for each kinase. Also, organelle markers were co-stained for some kinases to indicate specific localization.
description: TK family: The human kinome comprises 538 kinases playing essential cellular functions by catalyzing protein phosphorylations. Systematic annotation of subcellular spatial distribution of the kinome greatly facilitates investigation of normal and disease mechanisms. Here, we present Kinome Atlas (KA), an image-based map of the kinome annotated to 10 compartments of the cell. 456 epitope-tagged kinases, representing 85% of the human kinome, were expressed in HeLa cells and imaged by immunofluorescent microscopy under a unified condition. KA revealed kinase family-enriched subcellular localizations, and discovered a collection of new kinase localizations at mitochondria, plasma membrane, extracellular space, and other unique structures. This resource provides the first snapshot of the kinome under a unified condition, and is a key step toward comprehensive understanding of the spatial and temporal dynamics of the kinome in physiological and disease states.
description: Visualization methods: confocal microscopy
DOI: 10.6075/j0xs5trf
title: CIL: 50715, FIB-SEM Dataset of anti-PKHD1L1 Immuno-Gold Labeled Outer Hair Cell Stereocilia Bundles: 5.3_Cell_5_Stack_Filtered. In Cell Image Library

description: Images were acquired with FEI Helios FIB-SEM, using backscatter detector from an epoxy resin embedded inner ear Organ of Corti sample. 
5.3_Cell_5_Stack_Filtered is a multipage TIFF file filtered with unsharp filter (unit: 8 &gt; kernel: 3D, 5 &gt; standard deviation: 1.0 &gt; unsharp factor: 1.0).
This file is a part of Dataset 5, comprised of files related to the Cell #5 of current study. The numbering order of the files reflects the order of operations performed during the analysis.
description: FIB-SEM Dataset of anti-PKHD1L1 Immuno-Gold Labeled Outer Hair Cell Stereocilia Bundles. Postnatal day 4 mouse Inner Ear Organ of Corti labeled with anti-PKHD1L1 antibody (10 nm gold beads). The dataset represents the apical end of the Outer Hair Cell with the stereocilium bundle. Images were acquired with FEI Helios FIB-SEM, using backscatter detector from an epoxy resin embedded inner ear Organ of Corti sample.
description: Imaging mode: Serial Electron Microscopy; Focused Ion Beam Scanning Electron Mictoscopy (FIB-SEM)
Visualization methods: Heavy metal stain (Osmium Tetroxide, Potassium Ferrocyanide, Tannic Acid); Immunogold labeling with 10 nm gold beads
DOI: 10.6075/j0st7q06
title: CIL:48306, Sprague-Dawley rat. In Cell Image Library

description: Preparation: chemically fixed tissue
Imaging mode: confocal microscopy
description: The imaging protocol was based on topical application of 3 or 10 kDa dextran conjugated to Alexa Fluor 488 (Invitrogen, Carlsbad, CA, 125 μg/mL) via pipette to the tissue regions prior to imaging. Immediately following, images were acquired using the fiber-optics confocal microscopy system equipped with a custom fiber-optics microprobe (UltraMiniO; Mauna Kea Technologies, Paris, France). Using this imaging protocol, we acquired two-dimensional images sequences of the tissue regions at a lateral resolution (xy dimensions), optical sectioning (z), field of view (xy), frame rate, and z-scan range of 1.8 μm, 10 μm, 169 by 120 μm, 12 Hz and 50 μm, respectively. Example images from image sequences were stored as FCMtopical.
description: Images are acquired from fixed and living heart tissue using fiber-optics and laser-scanning confocal microscopy, respectively. Three sets of images denoted as CCM, FCMtopical, FCMcarrier were stored for subsequent analyses.
DOI: 10.6075/j0wd40np
title: CIL:2947, 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
Visualization methods: primary antibody plus labeled secondary antibody
Processing history: unprocessed raw data
description: Development of the axon and dendritic arbors in cultured hippocampal neurons after 3 days in vitro. MAP2 staining (red) highlights the dendrites, while microtubule staining (green) reveals both the axons and dendrites in the field of view. Neurons at 2, 3, 5 and 7 days in vitro are represented in this image group.

Detailed methods: 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 for tubulin (monoclonal DM1A, from Sigma with Alexa 488 conjugated secondary, excitation, 494, emission, 519 [Invitrogen, Molecular Probes]) and MAP2 (polyclonal Ab266, from S. Halpain with d549 conjugated secondary, excitation, 555, emission, 568, Jackson Immunoresearch). Images were acquired with a Leica DMRA microscope with a 20X (Fluotar, NA 0.5) lens, Photometrics CoolSnap ES CCD camera and MetaMorph software. Image generated with the MetaMorph color combine function.
DOI: 10.6075/j0mg7pkd
title: CIL:35835, Saccharomyces cerevisiae. In Cell Image Library

description: Preparation: living tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: fluorescence microscopy; phase contrast microscopy
Parameter imaged: fluorescence emission; elastic scattering of photons
Source of contrast: distribution of a specific protein; differences in amount of elastic light scattering
Visualization methods: EGFP
description: A time lapse experiment of Saccharomyces cerevisiae expressing GFP tagged Cln1. Cln 1 is a cyclin-dependent protein kinase regulator. These phase and GFP images are part of an image group containing CIL 35820-35839. Note that there are additional groups of images of other cell cycle regulator proteins by the same authors available in the Library.
description: Time-lapse images were collected on a DeltaVision system (Olympus IX71) with 60x/1.42 NA objective at 5 minute intervals. Please read the microscopy section of the referenced paper for details before image analysis.
DOI: 10.6075/j069733n
title: CIL: 52426, Homo sapiens, High-grade serious overian cancer. In Cell Image Library

description: One z layer of a z-stack at the given tile position
description: Imaging mode: Fluorescence in situ hybridization (FISH)
Visualization methods: Nikon Eclipse fluorescence inverted microscope equipped with a charge-coupled device camera (Andor Neo sCMOS), using filter sets for DAPI/ YGFP/TRITC/CY GFP with an objective lens (Plan Apo VC 100x, Nikon). Captured with 100x magnification of the objective and a pixel size of 0.07 microns
description: Tile x=5, y=3, z=2 from BL024199_Myc_Terc
DOI: 10.6075/j04748tp
title: CIL:35664, Saccharomyces cerevisiae. In Cell Image Library

description: A time lapse experiment of Saccharomyces cerevisiae expressing GFP tagged Cdc6. Cdc 6 is an essential ATP-binding protein required for DNA replication, component of the pre-replicative complex (pre-RC) which requires ORC to associate with chromatin and is in turn required for Mcm2-7p DNA association; homologous to S. pombe Cdc18p.These phase,gfp images are part of an image group that ranges from CIL:35660-35679. Note that there are additional groups showing time series of other cell cycle regulation proteins by the same authors in the Library.
description: Preparation: living tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: fluorescence microscopy; phase contrast microscopy
Parameter imaged: fluorescence emission; elastic scattering of photons
Source of contrast: distribution of a specific protein; differences in amount of elastic light scattering
Visualization methods: EGFP; visualization of contiguous regions
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements
description: The images were acquired using a 60x 1.42 NA objective lens on Delta Vision system equipped with CoolSNAP_HQ2 / HQ2-ICX285. Please see the microscopy section in the referenced manuscript for details for image analysis.
DOI: 10.6075/j0qj7g38
title: CIL:11828, Notophthalmus viridescens, Gallus gallus, erythrocyte. In Cell Image Library

description: In the upper panel, transmission electron microscopy reveals a tangled mass of ~30nm diameter nuclear chromatin fibers when the contents of the nucleus from erythrocytes of the newt Notophthalmus viridescens were spread on a water surface, fixed with formaldehyde, critical point dried, and metal shadowed. The lower panel shows chromatin from the nucleated erythrocyte of the chicken dispersed in low ionic strength, high pH buffer, centrifuged through a sucrose-formaldehyde cushion onto a carbon film and stained with uranyl acetate. When fully dispersed, the 'beads-on-a-string nucleosomal organization of chromatin is clearly evident.
description: Preparation: critical_point dried specimen; formaldehyde fixed tissue
Relation to intact cell: isolated subcellular component
Item type: film
Imaging mode: transmission electron microscopy (TEM); detection of electrons
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain; differences in deposition of metal shadow
Visualization methods: uranyl salt
Processing history: Image extracted from .pdf file of 'The Cell'
Data qualification: Processed
description: Figures 121 (upper panel, provided by Hans Ris) and 122 (lower, provided by Ada Olons) from Chapter 4 (Nucleus) of 'The Cell, 2nd Ed.' by Don W. Fawcett M.D. A PDF copy of the chapter is available on the ASCB's BioEDUCATE website.
DOI: 10.6075/j0df6qk7
title: CIL: 50786, Drosophila melanogaster. In Cell Image Library

description: Specimen preparation: Larval brains (LBs) were prepared from starved (amino acid-restricted) first instar (L1) larvae to enrich for quiescent neural stem cells. The LBs were glutaraldehyde-fixed, tannic acid and OsO4-stained, embedded in resin, thin-sectioned (60-70 nm) and stained with uranyl acetate/lead citrate, then observed by TEM.
description: Item type: Digital
Imaging mode: CM12 TEM equipped with AMT digital camera
description: We show in this study that brain and intestinal stem cells of Drosophila contain a new type of cytoplasmic protrusion which is enriched in mitochondria and that the mitochondria are probably dependent on microtubules for their distribution. The protrusions form mitochondria-enriched cytoplasmic bridges from the stem cells to their niche that we speculate are important in regulating stem cell quiescence and activation.
DOI: 10.5517/cc4crrz
title: CCDC 130471: Experimental Crystal Structure Determination

description: Related Article: Qing-chuan Yang, You-qi Tang, Wen-jun Yang, Hui-ying Chen|1998|Acta Crystallogr.,Sect.C:Cryst.Struct.Commun.|54|1532|doi:10.1107/S0108270198004818
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/cc4css1
title: CCDC 130503: Experimental Crystal Structure Determination

description: Related Article: R.Sankaranarayanan, D.Velmurugan, P.Murugan, N.Ramasubbu|1998|Acta Crystallogr.,Sect.C:Cryst.Struct.Commun.|54|1534|doi:10.1107/S0108270198005356
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/cc4cry5
title: CCDC 130477: Experimental Crystal Structure Determination

description: Related Article: J.J.Vittal, Shu-Gen Cao, Swee-Hock Goh, Goek-Kheng Tan, Keng-Yeow Sim|1998|Acta Crystallogr.,Sect.C:Cryst.Struct.Commun.|54|1536|doi:10.1107/S0108270198005691
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/cc4crz6
title: CCDC 130478: Experimental Crystal Structure Determination

description: Related Article: J.J.Vittal, Shu-Gen Cao, Swee-Hock Goh, Goek-Kheng Tan, Keng-Yeow Sim|1998|Acta Crystallogr.,Sect.C:Cryst.Struct.Commun.|54|1536|doi:10.1107/S0108270198005691
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/cc4cs08
title: CCDC 130479: Experimental Crystal Structure Determination

description: Related Article: J.J.Vittal, Shu-Gen Cao, Swee-Hock Goh, Goek-Kheng Tan, Keng-Yeow Sim|1998|Acta Crystallogr.,Sect.C:Cryst.Struct.Commun.|54|1536|doi:10.1107/S0108270198005691
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/cc4csv3
title: CCDC 130505: Experimental Crystal Structure Determination

description: Related Article: A.Waskowska|1998|Acta Crystallogr.,Sect.C:Cryst.Struct.Commun.|54|1540|doi:10.1107/S0108270198006118
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/cc4crs0
title: CCDC 130472: Experimental Crystal Structure Determination

description: Related Article: D.G.Morris, K.S.Ryder, R.A.Howie|1998|Acta Crystallogr.,Sect.C:Cryst.Struct.Commun.|54|1542|doi:10.1107/S0108270198006167
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/cc4cs7h
title: CCDC 130486: Experimental Crystal Structure Determination

description: Related Article: C.Samanta, A.K.Mukherjee, M.Mukherjee|1998|Acta Crystallogr.,Sect.C:Cryst.Struct.Commun.|54|1544|doi:10.1107/S0108270198003862
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/cc4crw3
title: CCDC 130475: Experimental Crystal Structure Determination

description: Related Article: K.W.Muir, C.S.Rodger, D.G.Morris, K.S.Ryder|1998|Acta Crystallogr.,Sect.C:Cryst.Struct.Commun.|54|1546|doi:10.1107/S0108270198006179
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/cc4crx4
title: CCDC 130476: Experimental Crystal Structure Determination

description: Related Article: J.Marek, J.Slanina|1998|Acta Crystallogr.,Sect.C:Cryst.Struct.Commun.|54|1548|doi:10.1107/S0108270198006489
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/cc3k7f9
title: CCDC 105940: Experimental Crystal Structure Determination

description: Related Article: T.Ziegler, F.Bien, C.Jurisch|1998|Tetrahedron:Asymm.|9|765|doi:10.1016/S0957-4166(98)00051-2
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/cc4csdn
title: CCDC 130491: Experimental Crystal Structure Determination

description: Related Article: Seik Weng Ng, Xiao-Ming Chen, Guang Yang|1998|Acta Crystallogr.,Sect.C:Cryst.Struct.Commun.|54|1389|doi:10.1107/S010827019800523X
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/cc3k6c6
title: CCDC 105907: Experimental Crystal Structure Determination

description: Related Article: T.Ziegler, F.Bien, C.Jurisch|1998|Tetrahedron:Asymm.|9|765|doi:10.1016/S0957-4166(98)00051-2
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/cc3k740
title: CCDC 105931: Experimental Crystal Structure Determination

description: Related Article: T.Ziegler, F.Bien, C.Jurisch|1998|Tetrahedron:Asymm.|9|765|doi:10.1016/S0957-4166(98)00051-2
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.