cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0qv3k8b
title: CIL:13575, Mus musculus, fibroblast. 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: single-spot confocal microscopy
Parameter imaged: fluorescence microscopy
Source of contrast: distribution of a specific protein; distribution of epitope; compartmentalization of stain or label
Visualization methods: Alexa Fluor 647; DsRed; EGFP; Helix pomatia agglutinin; Hoechst
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: Wild-type Arf1-GFP (Arf1(WT)-GFP) (gray) does not block redistribution of Helix Pomatia Lectin (HPL) (green) from Golgi to ER in Src-deficient SYF fibroblasts cotransfected with active Src (SrcE-DsRed) (red). HPL binds various glycans but the Tn antigen in particular. The Tn antigen refers to terminal α-linked N-acetyl galactosamine residues (GalNAc) linked to Ser or Thr residues. HPL indicates distribution of GalNac-Ts. Active Src is not enriched at the Golgi upon expression of Arf1(WT)-GFP. Cells were fixed for 10 min (4% paraformaldehyde) and permeabilized (0.2% Triton X-100) prior to staining with Hoechst (blue) and Alexa 647-conjugated-HPL. Cells were mounted onto glass slides using FluorSave (Merck) and imaged at room temperature using an inverted FluoView confocal microscope (model IX81; Olympus) with either a 60x objective (U Plan Super Apochromatic, UPLSAPO; NA 1.35) or 100x objective (UPLSAPO; NA 1.40) using Immersol oil. Microscope coupled with a CCD camera (model FVII). Images were acquired and processed using Olympus FV10-ASW software. Image corresponds to Fig 7D in J Cell Biol. 189: 843-858. 2010. Images in Fig 7 include CIL#s 13571, 13572, 13573, 13574, 13575, 13576, 13577.
DOI: 10.6075/j0kp80xr
title: CIL:13553, Homo sapiens, epithelial cell, cervical carcinoma. 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: single-spot confocal microscopy
Parameter imaged: fluorescence microscopy
Source of contrast: distribution of a specific protein; distribution of epitope; compartmentalization of stain or label
Visualization methods: Alexa Fluor 647; Alexa Fluor 488; primary antibody plus labeled secondary antibody; Helix pomatia agglutinin; Hoechst
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: Helix Pomatia Lectin (HPL) (green) is redistributed out of the Golgi (Giantin) (red) in HeLa cells upon EGF stimulation for 4h. The Tn antigen refers to terminal α-linked N-acetyl galactosamine residues (GalNAc) linked to Ser or Thr residues. HPL binds various glycans but the Tn antigen in particular. HeLa cells were serum starved overnight in DME (noFBS) and treated with human recombinant EGF (100 ng/ml; Sigma-Aldrich) and DMSO for 4h. Cells were fixed for 10 min (4% paraformaldehyde) and permeabilized (0.2% Triton X-100). Primary antibody staining followed the manufacturer's instructions. Cells were subsequently stained for 15–30 min with secondary Alexa Fluor–conjugated antibodies (Alexa 488 for anti-Giantin). Hoechst (blue) and Alexa 647-conjugated-HPL were added during secondary antibody incubations. Cells were mounted onto glass slides using FluorSave (Merck) and imaged at room temperature using an inverted FluoView confocal microscope (model IX81; Olympus) with fluorescence excitation at 405 nm, 488 nm, and 633 nm and either a 60x objective (U Plan Super Apochromatic [UPLSAPO]; NA 1.35) or 100x objective (UPLSAPO; NA 1.40) using Immersol oil. Microscope coupled with a CCD camera (model FVII). Images were acquired and processed using Olympus FV10-ASW software. Image corresponds to Fig 3A, top right panel, in J Cell Biol. 189: 843-858. 2010. Images in Fig 3 include CIL#s 13551, 13552, 13553, 13554.
DOI: 10.6075/j0m61j1j
title: CIL:40556, Paramecium multimicronucleatum, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: Monoclonal antibody, E30-2-1, was raised to antigen D6 that specifically labels acidosomes and DV-II. There was no label on the nascent vacuole membrane or ciliary membranes. This cell had been incubated in 1.1µm latex beads for 3 minutes and fixed without a chase. There is some gold over the cytosol but the nascent vacuole lumen is essentially free of label. TEM taken on 7/12/90 by R. Allen with Zeiss 10A operating at 80kV. Neg. 9,780X. Adapted with permission.
description: To label membranes inside the cell we used very lightly fixed cells (0.25% glutaraldehyde) that were then rapidly frozen in liquid nitrogen and sectioned later at -100oC. These frozen sections were picked up on drops of methylcellulose and transferred to a Formvar-supported grid. The sections were immunogold labeled (15nm gold) to show the location of the specific antigen inside the cell as well as on the cell surface. Microtome sections prepared at approximately 75nm thickness. The raw negative was scanned with an Epson Perfection V750 Pro and this high resolution image is best used for quantitative analysis. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
description: Preparation: glutaraldehyde fixed tissue; tissue in vitreous ice embedment; microtome-sectioned tissue; monoclonal antibody
Relation to intact cell: microtome-sectioned tissue
Item type: transmission electron microscopy (TEM); illumination by electrons
Imaging mode: detection of electrons; film
Parameter imaged: electron density; intrinsic mass distribution
Source of contrast: stain with broad specificity
Visualization methods: stain with broad specificity; uranyl salt; gold
Processing history: recorded image; film; Print from negative scanned for Photoshop.
Data qualification: Processed
DOI: 10.6075/j0x9290d
title: CIL:13543, Homo sapiens, epithelial cell, cervical carcinoma. 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: single-spot confocal microscopy
Parameter imaged: fluorescence microscopy
Source of contrast: distribution of a specific protein; distribution of epitope; compartmentalization of stain or label
Visualization methods: Alexa Fluor 647; Alexa Fluor 594; Alexa Fluor 488; primary antibody plus labeled secondary antibody; Helix pomatia agglutinin; Hoechst
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: Helix Pomatia Lectin (HPL) (green) staining is redistributed out of the Golgi of HeLa cells after EGF treatment for 4 h, while the Golgi marker Giantin (red) is unaffected. HPL binds various glycans but the Tn antigen in particular. The Tn antigen refers to terminal α-linked N-acetyl galactosamine residues (GalNAc) linked to Ser or Thr residues. Image also includes anti-GalNacT1 staining (gray). HeLa cells were serum starved overnight in DME (noFBS) and then treated with human recombinant EGF (100 ng/ml; Sigma-Aldrich) for 4h. Cells were fixed for 10 min (4% paraformaldehyde) and permeabilized (0.2% Triton X-100). Primary antibody staining followed the manufacturer's instructions. Cells were subsequently stained for 15–30 min with secondary Alexa Fluor–conjugated antibodies (Alexa 488 for anti-Giantin, Alexa 594 for anti GalNac-T1). Hoechst (blue) and Alexa 647-conjugated-HPL were added during secondary antibody incubations. Cells were mounted onto glass slides using FluorSave (Merck) and imaged at room temperature using an inverted FluoView confocal microscope (model IX81; Olympus) with fluorescence excitation at 488 nm, 561 nm, and 633 nm and either a 60x objective (U Plan Super Apochromatic [UPLSAPO]; NA 1.35) or 100x objective (UPLSAPO; NA 1.40) using Immersol oil. Microscope coupled with a CCD camera (model FVII). Images were acquired and processed using Olympus FV10-ASW software. Image corresponds to Fig 1B in J Cell Biol. 189: 843-858. 2010. Images in Fig 1 include CIL#s 13543, 13544, 13545, 13546.
DOI: 10.6075/j0sf2txv
title: CIL:13463, Saccharomyces cerevisiae S288c. In Cell Image Library

description: Kre2-GFP is not efficiently maintained in the Golgi apparatus when Pik1-mediated PtdIns4P synthesis ceases, implicating Pik1 signaling in retrograde trafficking of Golgi residents. In this image, Kre2-GFP is expressed in the isogenic control strain for the pik1-83 mutant, shifted to restrictive temperature of 37C for 1h. 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 Fig4D 37C PIK1 panel in J Cell Biol. 187: 967-975. 2009. Images in Fig 4D include CIL#s 13460, 13461, 13462, 13463, 13464, 13465, 13466, 13467.
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/j0t43sx1
title: CIL: 54622, Mus musculus, oocyte. In Cell Image Library

description: Imaging mode: whole mount confocal image
Visualization methods: Laser Scan Confocal; PMT
description: FIG.2B Changes in ER cluster morphology require gamete fusion.
description: Oocytes fixed with 2% paraformaldehyde and 1% picric acid. Immunolabelled with anti-Calreticulin (green), Alexafluor 568-phalloidin (red), and Hoechst 33342 (blue).
DOI: 10.6075/j069729x
title: CIL:13462, 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: Kre2-GFP is not efficiently maintained in the Golgi apparatus when Pik1-mediated PtdIns4P synthesis ceases, implicating Pik1 signaling in retrograde trafficking of Golgi residents. In this image, Kre2-GFP is expressed in the isogenic control strain for the pik1-83 mutant, at permissive temperature of 26C. 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 Fig4D 26C PIK1 panel in J Cell Biol. 187: 967-975. 2009. Images in Fig 4D include CIL#s 13460, 13461, 13462, 13463, 13464, 13465, 13466, 13467.
DOI: 10.6075/j06t0mp0
title: CIL:2907, Rattus, multipolar neuron. In Cell Image Library

description: Development of the axon and dendritic arbors in cultured hippocampal neurons after 2 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.
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
DOI: 10.6075/j06t0kcj
title: CIL:13475, Drosophila melanogaster, motor neuron. In Cell Image Library

description: The endosomal compartment is enlarged in the ema[1] mutant. Colocalization between DVGLUT (red) aggregates and the endosomal ESCRT protein Hrs (green, also known as Vps27) in motoneuron cell bodies of the ventral nerve cord of the ema[1] mutant. Wandering third instar larvae were dissected in ice-cold PBS and fixed with Bouin's solution for 5 min. Blocking and antibody incubation were performed in PBS containing 0.1% Triton X-100. anti-DVGLUT (Daniels et al., 2004) antibody was used at 1:10,000; anti-HRS-FL (Lloyd et al., 2002) was used at 1:1000. Secondary antibodies (Alexa 488-/Cy3-conjugated) were used at 1:1000. After staining, specimens were equilibrated in 70% glycerol in PBS and mounted with VectaShield (Vector Laboratories). Confocal images were acquired with a confocal microscope (model C1; Nikon) and accompanying EZ-C1 software using argon (excitation at 488 nm) and HeNe (excitation at 543 and 633 nm) lasers and a 60x Plan-Apochromat NA 1.4 objective (Nikon) at room temperature. Samples for each experiment were processed using the same confocal gain setting. Image corresponds to Figure 2A, bottom 3 panels in Kim et al. J Cell Biol. 188: 717-734. 2010.
description: Preparation: formaldehyde fixed tissue; detergent permeabilized
Relation to intact cell: whole mounted tissue
Item type: recorded image; photomultiplier tube (PMT)
Imaging mode: fluorescence microscopy; confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: primary antibody plus labeled secondary antibody; Alexa Fluor 488; Cy3
Data qualification: Raw
DOI: 10.6075/j0445k6p
title: CIL:9233, Homo sapiens, cervical carcinoma. In Cell Image Library

description: See Huang et al. 1997, The Dynamic Organization of the Perinucleolar Compartment in the Cell Nucleus J. Cell Biol 137: 965-974.
description: Immunofluorescence image of HeLa cell expressing a fusion protein of GFP-polypyrimidine tract binding protein showing the localization of the perinucleolar compartment (green area) at the periphery of the nucleolus (red region). The nuclear periphery is demarcated by immunolabeling of the nuclear lamina (blue).
description: Preparation: formaldehyde fixed tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: fluorescence microscopy; charge coupled device (CCD)
Parameter imaged: fluorescence microscopy
Source of contrast: fluorescence emission
Visualization methods: TexasRed; EGFP
DOI: 10.6075/j0qn65hk
title: CIL:13545, Homo sapiens, epithelial cell, cervical carcinoma. In Cell Image Library

description: Anti-Tn staining (green) co-localizes with Helix Pomatia Lectin (HPL) (red) at the Golgi (Giantin) (gray) in unstimulated HeLa cells. The Tn antigen refers to terminal α-linked N-acetyl galactosamine residues (GalNAc) linked to Ser or Thr residues. HPL binds various glycans but the Tn antigen in particular. HeLa cells were serum starved overnight in DME (noFBS). Cells were fixed for 10 min (4% paraformaldehyde) and permeabilized (0.2% Triton X-100). Primary antibody staining followed the manufacturer's instructions. Cells were subsequently stained for 15–30 min with secondary Alexa Fluor–conjugated antibodies (Alexa 488 for anti-Tn antigetn, Alexa 594 for anti Giantin), Hoechst (blue) and Alexa 647-conjugated-HPL was added during secondary antibody incubations. Cells were mounted onto glass slides using FluorSave (Merck) and imaged at room temperature using an inverted FluoView confocal microscope (model IX81; Olympus) with fluorescence excitation at 488 nm, 561 nm, and 633 nm and either a 60x objective (U Plan Super Apochromatic [UPLSAPO]; NA 1.35) or 100x objective (UPLSAPO; NA 1.40) using Immersol oil. Microscope coupled with a CCD camera (model FVII). Images were acquired and processed using Olympus FV10-ASW software. Image corresponds to Fig 1E in J Cell Biol. 189: 843-858. 2010. Images in Fig 1 include CIL#s 13543, 13544, 13545, 13546.
description: Preparation: formaldehyde fixed tissue; detergent permeabilized
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: single-spot confocal microscopy
Parameter imaged: fluorescence microscopy
Source of contrast: distribution of a specific protein; distribution of epitope; compartmentalization of stain or label
Visualization methods: Alexa Fluor 647; Alexa Fluor 594; Alexa Fluor 488; primary antibody plus labeled secondary antibody; Helix pomatia agglutinin; Hoechst
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
DOI: 10.15468/dl.27jwsu
title: Occurrence Download

description: A dataset containing 22 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is South America",
 "Country is Colombia",
 "GadmGid is COL.31_2",
 "Month is one of (January, February, March, April, May, June, July, August, September, October, November, December)",
 "OccurrenceStatus is Present",
 "TaxonKey is Chlorochrysa nitidissima",
 "Year 2010-2010"
 ]
}

 The dataset includes 22 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009269-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6075/j02806bs
title: CIL:13548, Homo sapiens, epithelial cell, cervical carcinoma. In Cell Image Library

description: After EGF treatment of HeLa cells for 4h, a significant amount of GalNac-T1 staining (red) is apparent in punctate and diffuse cytoplasmic cellular structures that stain positively for Helix Pomatia Lectin (HPL) (green). Anti-Giantin marks the Golgi (gray). The Tn antigen refers to terminal α-linked N-acetyl galactosamine residues (GalNAc) linked to Ser or Thr residues. HPL binds various glycans but the Tn antigen in particular. HeLa cells were serum starved overnight in DME (noFBS) and then treated with human recombinant EGF (100 ng/ml; Sigma-Aldrich) for 4h. Cells were fixed for 10 min (4% paraformaldehyde) and permeabilized (0.2% Triton X-100). Primary antibody staining followed the manufacturer's instructions. Cells were subsequently stained for 15–30 min with secondary Alexa Fluor–conjugated antibodies (Alexa 488 for anti-GalNac-T1, Alexa 594 for anti-Giantin). Hoechst (blue) and Alexa 647-conjugated-HPL was added during secondary antibody incubations. Cells were mounted onto glass slides using FluorSave (Merck) and imaged at room temperature using an inverted FluoView confocal microscope (model IX81; Olympus) with fluorescence excitation at 488 nm, 543 nm, and 633 nm and either a 60x objective (U Plan Super Apochromatic [UPLSAPO]; NA 1.35) or 100x objective (UPLSAPO; NA 1.40) using Immersol oil. Microscope coupled with a CCD camera (model FVII). Images were acquired and processed using Olympus FV10-ASW software. Image corresponds to Fig 2B in J Cell Biol. 189: 843-858. 2010. Images in Fig 2 include CIL#s 13547, 13548, 13549, 13550.
description: Preparation: formaldehyde fixed tissue; detergent permeabilized
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: single-spot confocal microscopy
Parameter imaged: fluorescence microscopy
Source of contrast: distribution of a specific protein; distribution of epitope; compartmentalization of stain or label
Visualization methods: Alexa Fluor 647; Alexa Fluor 594; Alexa Fluor 488; primary antibody plus labeled secondary antibody; Helix pomatia agglutinin; Hoechst
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
DOI: 10.6075/j0qr4vr8
title: CIL:48401, Mus musculus, CNS neuron (sensu Vertebrata). In Cell Image Library

description: Tomographic reconstruction of a dendrite and associated dendritic spines from a medium spiny neuron from the mouse nucleus accumens. This image is a maximum intensity projection of a segment of dendrite in a 2 um section. The cell was filled by intracellular injection of Lucifer Yellow dye and photooxidized. This reconstructed image has been downsampled from the raw data image, which can be accessed using the link provided to the Cell Centered Database.
description: Relation to intact cell: microtome-sectioned tissue
Item type: recorded image
Imaging mode: detection of electrons; illumination by electrons
Parameter imaged: electron density
Data qualification: Processed
description: The tomogram was generated using an JEOL4000 IVEM. Single tilt images spanned -60 to 60° in 2° increments. Magnification, 3000X; accelerating voltage, 400KeV.
DOI: 10.6075/j0gx49bt
title: CIL:13551, Homo sapiens, epithelial cell, cervical carcinoma. In Cell Image Library

description: Helix Pomatia Lectin (HPL) (green) redistribution out of the Golgi (Giantin) (red) in HeLa cells upon EGF stimulation for 4 h is inhibited by co-treatment of Src Kinase Inhibitor, SU6656. The Tn antigen refers to terminal α-linked N-acetyl galactosamine residues (GalNAc) linked to Ser or Thr residues. HPL binds various glycans but the Tn antigen in particular. HeLa cells were serum starved overnight in DME (noFBS) and treated with human recombinant EGF (100 ng/ml; Sigma-Aldrich) and 10 µM SU6656; Merck for 4h. Cells were fixed for 10 min (4% paraformaldehyde) and permeabilized (0.2% Triton X-100). Primary antibody staining followed the manufacturer's instructions. Cells were subsequently stained for 15–30 min with secondary Alexa Fluor–conjugated antibodies (Alexa 488 for anti-Giantin). Hoechst (blue) and Alexa 647-conjugated-HPL were added during secondary antibody incubations. Cells were mounted onto glass slides using FluorSave (Merck) and imaged at room temperature using an inverted FluoView confocal microscope (model IX81; Olympus) with fluorescence excitation at 405 nm, 488 nm, and 633 nm and either a 60x objective (U Plan Super Apochromatic [UPLSAPO]; NA 1.35) or 100x objective (UPLSAPO; NA 1.40) using Immersol oil. Microscope coupled with a CCD camera (model FVII). Images were acquired and processed using Olympus FV10-ASW software. Image corresponds to Fig 3A, bottom right, Src Inhibitor treated/4 hours EGF, in J Cell Biol. 189: 843-858. 2010. Images in Fig 3 include CIL#s 13551, 13552, 13553, 13554.
description: Preparation: formaldehyde fixed tissue; detergent permeabilized
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: single-spot confocal microscopy
Parameter imaged: fluorescence microscopy
Source of contrast: distribution of a specific protein; distribution of epitope; compartmentalization of stain or label
Visualization methods: Alexa Fluor 647; Alexa Fluor 488; primary antibody plus labeled secondary antibody; Helix pomatia agglutinin; Hoechst
Data qualification: Raw;spatialmeasurements;intensitiesquantitation