cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0vt1qqz
title: CIL:38602, Homo sapiens, fibroblast. In Cell Image Library

description: Preparation: formaldehyde fixed tissue
Relation to intact cell: dispersed cells in vitro
Item type: portrayed image
Imaging mode: PALM (photoactivation localization microscopy)
Parameter imaged: recorded image
Source of contrast: fluorescence emission
Visualization methods: psCFP2; tdEos
Processing history: probability density map
description: This photoactivation localization microscopy (PALM) image of tdEos-paxillin (green) and PsCFP20-zyxin (red) demonstrates that these two focal adhesion proteins are have very little over-lap when visualized with super-resolution. In contrast, when the same field is visualized with total internal reflection (TIRF) microscopy, the two proteins appear almost completely colocalized CIL 38604. Note the differential interference contrast (DIC) image corresponding to the same image field is also available as CIL 38603. Bar is 2 microns. Image made available by Catherine and James Galbraith and corresponds to Figure 4 in PNAS U S A. 2007 Dec 18;104(51):20308-13.
DOI: 10.6075/j0n58k1k
title: CIL:38652, Homo sapiens, fibroblast. In Cell Image Library

description: Preparation: formaldehyde fixed tissue
Relation to intact cell: dispersed cells in vitro
Item type: portrayed image; recorded image
Imaging mode: PALM (photoactivation localization microscopy); TIRF (total internal reflection)
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: CeruleanFP; Dronpa; tdEos
Processing history: probability density map
Data qualification: Processed
description: This image combines total internal reflection microscopy (TIRF) of mCerulean-actin (blue) with photoactivation localization microscopy (PALM) image of tdEos-vinculin (red) and Dronpa-paxillin (green). Vinculin and paxillin are organized into focal adhesions at the ends of actin bundles. A higher magnification of several adhesion complexes (CIL 38651) clearly shows that vinculin and paxillin are segregated into interlocking microdomains within focal adhesions. Bar is 2 microns. Image made available by Catherine and James Galbraith and corresponds to Figure 5 in PNAS U S A. 2007 Dec 18;104(51):20308-13.
DOI: 10.6075/j0gb22ps
title: CIL:38600, Homo sapiens, fibroblast. In Cell Image Library

description: Preparation: formaldehyde fixed tissue
Relation to intact cell: dispersed cells in vitro
Item type: portrayed image
Imaging mode: PALM (photoactivation localization microscopy)
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: Dronpa; tdEos
Processing history: probability density map
description: Photoactivation localization microscopy image (PALM) of a human foreskin fibroblast expressing Dronpa-actin (green) and tdEos-paxillin (red). Paxillin assembles in fibrillar-like adhesions that run parallel to ventral actin fibers and cluster near the cell periphery to form larger adhesion complexes. The differential interference contrast image (DIC) corresponding to this field is CIL 38601. Image made available by Catherine and James Galbraith and corresponds to Figure 2 in PNASi U S A. 2007 Dec 18;104(51):20308-13 and corresponds to Figure 2 in PNAS U S A. 2007 Dec 18;104(51):20308-13.
DOI: 10.6075/j0nk3dgk
title: CIL: 51228, Mus musculus, RAW 264.7 TIB-71. In Cell Image Library

description: A novel cell population analysis to quantify both initial and long-term drug effects, namely pseudopod adaptation and recovery following an initial drug-induced perturbation, adding drug slowly in 1/4 increments over 90 minutes.
description: Imaging mode: DICM
Visualization methods: Spinning disc confocal DICM & widefield DICM Using a Nikon TiE microscope equipped with a 40x, 0.95 N.A. objective and a Hamamatsu ORCA-Flash 4.0 V3 Digital CMOS camera, or a Nikon TiE spinning-disc confocal microscope equipped with a Yokogawa CSU-X1 scanning unit, an Andor iXon 888 EMCCD camera, and a 60x, 1.3 N.A. water-immersion objective or a 40x, 0.95 N.A. objective
description: ~1200 cells were imaged on glass. More gradual additions of drug or carrier were carried out in four equal increments at 0, 30, 60, 90 min, together yielding the same final drug concentration indicated in rapid addition studies. The subpopulation of ~100 cells with extended, leading edge pseudopods at t = 0 were imaged and counted in each unit area at the indicated timepoints during a 125 min observation period T=37C

Images are provided as uncorrected, 16 bit .nd2 files to preserve all original data. To view these .nd2 files:
1. Download ImageJ viewer at (https://imagej.nih.gov/ij/download.html)
2. Download the BioFormats.jar package at (https://www.openmicroscopy.org/bio-formats/downloads/)
3. Open the ImageJ directory after installation and drag the extracted BioFormats.jar package into the "Plugins" subdirectory
4. Open an .nd2 image using imageJ and select opening options when prompted, if desired. If no modifications are desired, select "OK"
5. The 16 bit image will typically look dark and will require brightness adjustment.
6. In the ImageJ toolbar, select Image &gt;&gt; Adjust &gt;&gt; Brightness/Contrast and select "Auto", or manually set the brightness and contrast.
DOI: 10.6075/j0jd4w4m
title: CIL:38664, Rattus rattus, glandular epithelial cell, milk secreting cell, mammary alveolar cell. In Cell Image Library

description: Immunoelectron microscopy of mammary gland tissue from lactating rats investigating potential structural interactions between mature lipid droplets and elements of the trans-Golgi network, identified by TGN38 (a transmembrane trans-Golgi protein; larger gold particles) and cation-dependent mannose-6-phosphate receptor (an integral membrane protein that localizes to the trans-Golgi
 reticulum, endosomes, and the plasma membrane; smaller gold particles) staining. Note that trans‚ÄêGolgi cisternae in lactating mammary cells contain large amounts of casein and other milk proteins and are grossly expanded due to the osmolarity of the secreted fluid.
description: Preparation: cryostat-sectioned tissue; formaldehyde fixed tissue; embedded tissue; methylcellulose embedded
Relation to intact cell: sectioned tissue
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM); illumination by electrons; detection of electrons
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain; distribution of a specific protein
Visualization methods: gold; uranyl salt; primary antibody plus labeled secondary antibody
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: Tissue was processed for immunoelectron microscopy using a modified Tokuyasu method. Briefly, minced tissue was fixed in 4% paraformaldehyde containing 5% sucrose and 100 mM HEPES and infiltrated with PBS containing 2.1 M sucrose over 10 h, with repeated solution changes. Fixed tissue was transferred to an aluminum cryosectioning stub (Ted Pella, Inc., Redding, CA) and immediately frozen in liquid nitrogen. Semithin (90 nm) cryosections were cut at -110C with an UltraCut UCT/FCS cryomicrotome (Leica), using a diamond knife (Diatome) and transferred to a Formvar-coated, carbon-coated, glow-discharged 100-mesh copper-rhodium electron microscopy grid. Following blocking of nonspecific antibody binding sites with 10% calf serum in PBS, the sections were labeled by sequential incubation with antibodies to cation-dependent mannose-6-phosphate receptor (rabbit) and TGN38 (mouse monoclonal 2F7) and colloidal gold-conjugated secondary antibodies (10 nm anti-rabbit, 15 nm anti-mouse; Ted Pella Inc., Redding, CA) and then negatively stained and embedded with 1% uranyl acetate, 1% methylcellulose in distilled water. Samples were viewed in a Philips CM10 electron microscope, and images were collected digitally. Magnification 28,500 X. See Ladinsky and Howell (2007) for more information on methods used.
DOI: 10.6075/j0m61hxs
title: CIL:38651, Homo sapiens, fibroblast. In Cell Image Library

description: Preparation: formaldehyde fixed tissue
Relation to intact cell: dispersed cells in vitro
Item type: portrayed image
Imaging mode: PALM (photoactivation localization microscopy)
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: Dronpa; tdEos
Processing history: probability density map
Data qualification: Processed
description: This photoactivation localization microscopy (PALM) image of tdEos-vinculin (red) and Dronpa-paxillin (green) illustrates that vinculin and paxillin are segregated into interlocking microdomains within focal adhesions. A lower magnification view that orients the adhesions on actin bundles is available as CIL 38652. Bar is 1 micron. Image made available by Catherine and James Galbraith and corresponds to Figure 5 in PNAS U S A. 2007 Dec 18;104(51):20308-13.
DOI: 10.6084/m9.figshare.30441416
title: <b>Genetic variations in </b><b><i>AAK1</i></b><b> and</b><b><i> ADAM17 </i></b><b>genes associated with Circulatory Cytokines changes influence COVID-19 Susceptibility and Severity</b>

description: Our study investigates the role of specific single-nucleotide variants (SNVs) in AAK1, ADAM17, and CD209, genes implicated in SARS-CoV-2 entry and immune regulation. Using targeted next-generation sequencing in a Middle-Eastern cohort of 96 COVID-19 patients with varying disease severity and 69 matched controls. We identified significant associations between specific variants of ADAM17, and AAK1 in relation to COVID-19 susceptibility. Moreover, correlations between these variants and key inflammatory cytokines, suggesting functional regulatory impacts supported by in-silico predictions. These findings emphasize potential genetic biomarkers that influence SARS-CoV-2 susceptibility, disease severity, and immune response, providing insights into host-pathogen interactions and personalized treatment strategies.
DOI: 10.6084/m9.figshare.30441416.v1
title: <b>Genetic variations in </b><b><i>AAK1</i></b><b> and</b><b><i> ADAM17 </i></b><b>genes associated with Circulatory Cytokines changes influence COVID-19 Susceptibility and Severity</b>

description: Our study investigates the role of specific single-nucleotide variants (SNVs) in AAK1, ADAM17, and CD209, genes implicated in SARS-CoV-2 entry and immune regulation. Using targeted next-generation sequencing in a Middle-Eastern cohort of 96 COVID-19 patients with varying disease severity and 69 matched controls. We identified significant associations between specific variants of ADAM17, and AAK1 in relation to COVID-19 susceptibility. Moreover, correlations between these variants and key inflammatory cytokines, suggesting functional regulatory impacts supported by in-silico predictions. These findings emphasize potential genetic biomarkers that influence SARS-CoV-2 susceptibility, disease severity, and immune response, providing insights into host-pathogen interactions and personalized treatment strategies.
DOI: 10.6075/j0jm2903
title: CIL:38667, Rattus rattus, glandular epithelial cell, milk secreting cell, mammary alveolar cell. In Cell Image Library

description: Preparation: cryostat-sectioned tissue; formaldehyde fixed tissue; embedded tissue; methylcellulose embedded
Relation to intact cell: sectioned tissue
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM); illumination by electrons; detection of electrons
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain; distribution of a specific protein
Visualization methods: gold; uranyl salt; primary antibody plus labeled secondary antibody
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: Tissue was processed for immunoelectron microscopy using a modified Tokuyasu method. Briefly, minced tissue was fixed in 4% paraformaldehyde containing 5% sucrose and 100 mM HEPES and infiltrated with PBS containing 2.1 M sucrose over 10 h, with repeated solution changes. Fixed tissue was transferred to an aluminum cryosectioning stub (Ted Pella, Inc., Redding, CA) and immediately frozen in liquid nitrogen. Semithin (90 nm) cryosections were cut at -110C with an UltraCut UCT/FCS cryomicrotome (Leica), using a diamond knife (Diatome) and transferred to a Formvar-coated, carbon-coated, glow-discharged 100-mesh copper-rhodium electron microscopy grid. Following blocking of nonspecific antibody binding sites with 10% calf serum in PBS, the sections were labeled by sequential incubation with antibodies to cation-dependent mannose-6-phosphate receptor (rabbit) and TGN38 (mouse monoclonal 2F7) and colloidal gold-conjugated secondary antibodies (10 nm anti-rabbit, 15 nm anti-mouse; Ted Pella Inc., Redding, CA) and then negatively stained and embedded with 1% uranyl acetate, 1% methylcellulose in distilled water. Samples were viewed in a Philips CM10 electron microscope, and images were collected digitally. Magnification 21,000 X. See Ladinsky and Howell (2007) for more information on methods used.
description: Immunoelectron microscopy of mammary gland tissue from lactating rats investigating potential structural interactions between mature lipid droplets and elements of the trans-Golgi network, identified by TGN38 (a transmembrane trans-Golgi protein; larger gold particles) and cation-dependent mannose-6-phosphate receptor (an integral membrane protein that localizes to the trans-Golgi
 reticulum, endosomes, and the plasma membrane; smaller gold particles) staining. Note that trans‚ÄêGolgi cisternae in lactating mammary cells contain large amounts of casein and other milk proteins and are grossly expanded due to the osmolarity of the secreted fluid.
DOI: 10.6075/j0zp45gw
title: CIL:38670, Rattus rattus, glandular epithelial cell, milk secreting cell, mammary alveolar cell. In Cell Image Library

description: Immunoelectron microscopy of mammary gland tissue from lactating rats investigating potential structural interactions between mature lipid droplets and elements of the trans-Golgi network, identified by TGN38 (a transmembrane trans-Golgi protein; larger gold particles) and cation-dependent mannose-6-phosphate receptor (an integral membrane protein that localizes to the trans-Golgi
 reticulum, endosomes, and the plasma membrane; smaller gold particles) staining. Note that trans‚ÄêGolgi cisternae in lactating mammary cells contain large amounts of casein and other milk proteins and are grossly expanded due to the osmolarity of the secreted fluid.
description: Tissue was processed for immunoelectron microscopy using a modified Tokuyasu method. Briefly, minced tissue was fixed in 4% paraformaldehyde containing 5% sucrose and 100 mM HEPES and infiltrated with PBS containing 2.1 M sucrose over 10 h, with repeated solution changes. Fixed tissue was transferred to an aluminum cryosectioning stub (Ted Pella, Inc., Redding, CA) and immediately frozen in liquid nitrogen. Semithin (90 nm) cryosections were cut at -110C with an UltraCut UCT/FCS cryomicrotome (Leica), using a diamond knife (Diatome) and transferred to a Formvar-coated, carbon-coated, glow-discharged 100-mesh copper-rhodium electron microscopy grid. Following blocking of nonspecific antibody binding sites with 10% calf serum in PBS, the sections were labeled by sequential incubation with antibodies to cation-dependent mannose-6-phosphate receptor (rabbit) and TGN38 (mouse monoclonal 2F7) and colloidal gold-conjugated secondary antibodies (10 nm anti-rabbit, 15 nm anti-mouse; Ted Pella Inc., Redding, CA) and then negatively stained and embedded with 1% uranyl acetate, 1% methylcellulose in distilled water. Samples were viewed in a Philips CM10 electron microscope, and images were collected digitally. Magnification 15,500 X. See Ladinsky and Howell (2007) for more information on methods used.
description: Preparation: cryostat-sectioned tissue; formaldehyde fixed tissue; embedded tissue; methylcellulose embedded
Relation to intact cell: sectioned tissue
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM); illumination by electrons; detection of electrons
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain; distribution of a specific protein
Visualization methods: gold; uranyl salt; primary antibody plus labeled secondary antibody
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
DOI: 10.6075/j0v987c5
title: CIL:38666, Rattus rattus, glandular epithelial cell, milk secreting cell, mammary alveolar cell. In Cell Image Library

description: Preparation: cryostat-sectioned tissue; formaldehyde fixed tissue; embedded tissue; methylcellulose embedded
Relation to intact cell: sectioned tissue
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM); illumination by electrons; detection of electrons
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain; distribution of a specific protein
Visualization methods: gold; uranyl salt; primary antibody plus labeled secondary antibody
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: Immunoelectron microscopy of mammary gland tissue from lactating rats investigating potential structural interactions between mature lipid droplets and elements of the trans-Golgi network, identified by TGN38 (a transmembrane trans-Golgi protein; larger gold particles) and cation-dependent mannose-6-phosphate receptor (an integral membrane protein that localizes to the trans-Golgi
 reticulum, endosomes, and the plasma membrane; smaller gold particles) staining. Note that trans‚ÄêGolgi cisternae in lactating mammary cells contain large amounts of casein and other milk proteins and are grossly expanded due to the osmolarity of the secreted fluid.
description: Tissue was processed for immunoelectron microscopy using a modified Tokuyasu method. Briefly, minced tissue was fixed in 4% paraformaldehyde containing 5% sucrose and 100 mM HEPES and infiltrated with PBS containing 2.1 M sucrose over 10 h, with repeated solution changes. Fixed tissue was transferred to an aluminum cryosectioning stub (Ted Pella, Inc., Redding, CA) and immediately frozen in liquid nitrogen. Semithin (90 nm) cryosections were cut at -110C with an UltraCut UCT/FCS cryomicrotome (Leica), using a diamond knife (Diatome) and transferred to a Formvar-coated, carbon-coated, glow-discharged 100-mesh copper-rhodium electron microscopy grid. Following blocking of nonspecific antibody binding sites with 10% calf serum in PBS, the sections were labeled by sequential incubation with antibodies to cation-dependent mannose-6-phosphate receptor (rabbit) and TGN38 (mouse monoclonal 2F7) and colloidal gold-conjugated secondary antibodies (10 nm anti-rabbit, 15 nm anti-mouse; Ted Pella Inc., Redding, CA) and then negatively stained and embedded with 1% uranyl acetate, 1% methylcellulose in distilled water. Samples were viewed in a Philips CM10 electron microscope, and images were collected digitally. Magnification 21,000 X. See Ladinsky and Howell (2007) for more information on methods used.
DOI: 10.6075/j0f18xp0
title: CIL:36766, Paramecium caudatum, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: Standard glutaraldehyde fixation followed by osmium tetroxide, dehydrated in alcohol and embedded in an epoxy resin. Microtome sections prepared at approximately 75nm thickness. The negative was printed to paper and the image was scanned to Photoshop. This digitized image is available for qualitative analysis. There is a high resolution version of this image in the library (CIL:39127) which is available for quantitative analysis. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
description: Ciliates such as Paramecium have specialized sites for endocytosis and exocytosis. Most of their surface is not available for internalization of membrane because of the underlying alveolar sac system. However to the right of each basal body or pair of basal bodies is an indentation of the plasma membrane called the parasomal sac. This penetrates through the septum and ends as a coated pit. This micrograph also illustrates the normal view of mitochondria in P. caudatum which are filled with tubular cristae. In cacodylate-buffered fixations the cytosol contains abundant electron-opaque glycogen storage granules which seem to be removed during collidine-buffered fixations. TEM taken on 5/28/69 by R. Allen with Philips 300 operating at 60kV. Neg. 14,800X. Bar = 0.5µm.
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
Source of contrast: intrinsic mass distribution; 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/j0bv7fhx
title: CIL:36767, Paramecium caudatum, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue; osmium tetroxide fixed tissue; tissue in epoxy resin embedment; microtome-sectioned tissue
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
Source of contrast: stain with broad specificity
Visualization methods: stain with broad specificity; uranyl salt; lead salt; osmium tetroxide
Processing history: recorded image; film; Print from negative scanned for Photoshop.
Data qualification: Processed
description: Receptor mediated endocytosis is a process in which extracellular molecules are taken into the cell via coated vesicles that pinch from the plasma membrane. In Paramecium the resulting vesicles fuse with flattened cisterna called early endosomes. Early endosomes accumulate just under the cortex of the cell. Sorting of proteins destined to be returned to the plasma membrane after separating from cargo occurs in the early endosomes and is facilitated by the formation of secondary coated pits and vesicles on the early endosomes that are smaller than the coated and uncoated preendosomal vesicles that arise from the plasma membrane. These small coated pits pinch off and subsequently lose their coats to form carrier vesicles that are roughly 100nm in diameter. These vesicles move deeper into the cell where they bind to microtubular ribbons. TEM taken on 11/4/68 by R. Allen with Philips 300 operating at 60kV. Neg. 20,500X. Bar = 0.5µm.
description: Standard glutaraldehyde fixation followed by osmium tetroxide, dehydrated in alcohol and embedded in an epoxy resin. Microtome sections prepared at approximately 75nm thickness. The negative was printed to paper and the image was scanned to Photoshop. This digitized image is available for qualitative analysis. There is a high resolution version of this image in the library (CIL:39139) which is available for quantitative analysis. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).