cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0bg2mrf
title: CIL:26530, Mus musculus, fibroblast. In Cell Image Library

description: Cells were cultured in DME (Invitrogen) supplemented with 10% fetal bovine serum and 100 U/ml penicillin/streptomycin (Invitrogen) at 37°C in a humidified 5% CO2 incubator. For transfections, cells in 60-mm-diameter dishes or on fibronectin-coated coverslips were incu- bated with a mixture of DNA and LipofectAMINE 2000 (Invitrogen) according to the manufacturer's instructions. The cDNA for MLC was subcloned into pCMV-myc (Takara Bio Inc.). Mutant constructs of MLC were generated using a QuikChange site-directed mutagenesis kit (Agilent Technologies) according to the manufacturer's protocol. In this myc-tagged MLC mutant, Ser1/Ser2 were replaced by alanines. In some experimental conditions, 16 h after replating onto fibronectin-coated coverslips, cells were treated with 50 ng/ml PDGF for 20 min. Cells were fixed 24–48 h after transfection using 3.7% paraformaldehyde in PBS for 15 min, permeabilized using 0.2% Triton X-100 in PBS for 2 min, blocked with 2% BSA in PBS, and co-stained for MLC (green), TRIO (red), and actin (blue). Images were captured by Zeiss LSM 710 confocal microscope with Plan-Apochromat 63X objective.
description: Preparation: formaldehyde fixed tissue; detergent permeabilized
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope; distribution of a specific protein
Visualization methods: Alexa Fluor 488; Alexa Fluor 546; phalloidin
Data qualification: Raw
description: To study the molecular mechanism by which nonmuscle myosin II (MII) regulates protrusion and adhesion dynamics in migrating cells, NIH3T3 cells were transfected with myc-tagged phosphomimetic constitutively active MLC mutants (MLCaa, green). After 20' exposure to PDGF, which induces myosin-inactivation, stress fiber disassembly, and stimulates fibroblast motility, the cells were fixed and co-stained for TRIO (a multifunctional, multidomain Rho guanine nucleotide exchange factor, red) and filamentous actin (blue). These findings help elucidate a functional link between MII and Rac1/Cdc42 GTPases, which may regulate protrusion/adhesion dynamics in migrating cells. This image is original data from Fig. S5 "Expression of active MLC mutants inhibits the dissociation of MII–Trio complex," in J. Cell Biol. 2010. Vol. 190(4):663–674
DOI: 10.6075/j0w66jn0
title: CIL:26533, 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: confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope; distribution of a specific protein
Visualization methods: Alexa Fluor 488; Alexa Fluor 546; phalloidin
Data qualification: Raw
description: Cells were cultured in DME (Invitrogen) supplemented with 10% fetal bovine serum and 100 U/ml penicillin/streptomycin (Invitrogen) at 37°C in a humidified 5% CO2 incubator. For transfections, cells in 60-mm-diameter dishes or on fibronectin-coated coverslips were incu- bated with a mixture of DNA and LipofectAMINE 2000 (Invitrogen) according to the manufacturer's instructions. The cDNA for MLC was subcloned into pCMV-myc (Takara Bio Inc.). Mutant constructs of MLC were generated using a QuikChange site-directed mutagenesis kit (Agilent Technologies) according to the manufacturer's protocol. In this myc-tagged MLC mutant, Ser1/2 were replaced by alanines, and expressed in NIH3T3 cells.
In some experimental conditions, 16 h after replating onto fibronectin-coated coverslips, cells were treated with 50 ng/ml PDGF for 20 min. Cells were fixed 24–48 h after transfection using 3.7% paraformaldehyde in PBS for 15 min, permeabilized using 0.2% Triton X-100 in PBS for 2 min, blocked with 2% BSA in PBS, and co-stained for MLC (green), TRIO (red), and actin (blue). Images were captured by Zeiss LSM 710 confocal microscope with Plan-Apochromat 63X objective.
description: To study the molecular mechanism by which nonmuscle myosin II (MII) regulates protrusion and adhesion dynamics in migrating cells, NIH3T3 cells were transfected with phosphomimetic constitutively active MLC mutants (MLCaa, green) and co-stained for βPIX (a Rac1/Cdc42-specific GEF highly implicated in cell motility, red) and filamentous actin (blue). These findings help elucidate a functional link between MII and Rac1/Cdc42 GTPases, which may regulate protrusion/adhesion dynamics in migrating cells. This image is the original data file from Fig. 7C,"PDGF-induced dissociation of the MII–βPIX complex," in J. Cell Biol. 2010. Vol. 190(4):663–674
DOI: 10.6075/j08g8jgp
title: CIL:26528, Mus musculus, fibroblast. In Cell Image Library

description: To study the molecular mechanism by which nonmuscle myosin II (MII) regulates protrusion and adhesion dynamics in migrating cells, NIH3T3 cells were transfected with myc-tagged myosin light chain (MLC, green). After 20' exposure to PDGF, which induces myosin-inactivation, stress fiber disassembly, and stimulates fibroblast motility, the cells were fixed and co-stained for TRIO (a multifunctional, multidomain Rho guanine nucleotide exchange factor, red) and filamentous actin (blue). These findings help elucidate a functional link between MII and Rac1/Cdc42 GTPases, which may regulate protrusion/adhesion dynamics in migrating cells. This image is the original data file from Fig. S5, "Expression of active MLC mutants inhibits the dissociation of MII–Trio complex," in J. Cell Biol. 2010. Vol. 190(4):663–674.
description: Preparation: formaldehyde fixed tissue; detergent permeabilized
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope; distribution of a specific protein
Visualization methods: Alexa Fluor 488; Alexa Fluor 546; phalloidin
Data qualification: Raw
description: Cells were cultured in DME (Invitrogen) supplemented with 10% fetal bovine serum and 100 U/ml penicillin/streptomycin (Invitrogen) at 37°C in a humidified 5% CO2 incubator. For transfections, cells in 60-mm-diameter dishes or on fibronectin-coated coverslips were incu- bated with a mixture of DNA and LipofectAMINE 2000 (Invitrogen) according to the manufacturer's instructions. In some experimental conditions, 16 h after replating onto fibronectin-coated coverslips, cells were treated with 50 ng/ml PDGF for 20 min. Cells were fixed 24–48 h after transfection using 3.7% paraformaldehyde in PBS for 15 min, permeabilized using 0.2% Triton X-100 in PBS for 2 min, blocked with 2% BSA in PBS, and co-stained for MLC (green), TRIO (red), and actin (blue). Images were captured by Zeiss LSM 710 confocal microscope with Plan-Apochromat 63X objective.
DOI: 10.6075/j0jw8crt
title: CIL:26527, Mus musculus, fibroblast. In Cell Image Library

description: Cells were cultured in DME (Invitrogen) supplemented with 10% fetal bovine serum and 100 U/ml penicillin/streptomycin (Invitrogen) at 37°C in a humidified 5% CO2 incubator. For transfections, cells in 60-mm-diameter dishes or on fibronectin-coated coverslips were incu- bated with a mixture of DNA and LipofectAMINE 2000 (Invitrogen) according to the manufacturer's instructions. In some experimental conditions, 16 h after replating onto fibronectin-coated coverslips, cells were treated with 50 ng/ml PDGF for 20 min. Cells were fixed 24–48 h after transfection using 3.7% paraformaldehyde in PBS for 15 min, permeabilized using 0.2% Triton X-100 in PBS for 2 min, blocked with 2% BSA in PBS, and co-stained for MLC (green), TRIO (red), and actin (blue, Alexafluor350 conjugated phalloidin). Images were captured by Zeiss LSM 710 confocal microscope with Plan-Apochromat 63X objective.
description: Preparation: formaldehyde fixed tissue; detergent permeabilized
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope; distribution of a specific protein
Visualization methods: Alexa Fluor 488; Alexa Fluor 546; phalloidin
Data qualification: Raw
description: To study the molecular mechanism by which nonmuscle myosin II (MII) regulates protrusion and adhesion dynamics in migrating cells, NIH3T3 cells were transfected with myc-tagged myosin light chain (MLC, green) and co-stained for TRIO (a multifunctional, multidomain Rho guanine nucleotide exchange factor, red) and filamentous actin (blue). These findings help elucidate a functional link between MII and Rac1/Cdc42 GTPases, which may regulate protrusion/adhesion dynamics in migrating cells. This image is original data from Fig. S5 "Expression of active MLC mutants inhibits the dissociation of MII–Trio complex," in J. Cell Biol. 2010. Vol. 190(4):663–674.
DOI: 10.6075/j0vd6xjz
title: CIL:2653, Caenorhabditis elegans. In Cell Image Library

description: Terminal Bulb is a dataset of DIC (differential interference contrast) 20x microscopy images of the pharynx terminal bulb of C. elegans at different ages (0, 2, 4, 6, 8, 10, 12 days). Note that the data sets for each age can be found by searching for a featured image from each set: CIL 1587, 1694, 1905, 2213, 2622, 2544, and 2606, respectively.
description: Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: differential interference contrast microscopy
Parameter imaged: optical path length gradient
Source of contrast: boundaries between regions with different refractive index
Visualization methods: visualization of contiguous regions
Processing history: unprocessed raw data
description: The purpose of the dataset C. elegans terminal bulb aging is to deduce the age of the nemathode based on images of the pharynx terminal bulb (part of the eating apparatus). Images of C. elegans were taken at different chronological ages. This image is part of the day 12 data set. Note that the morphological and chronological ages are not fully correlated due to the variability among individuals even though the individuals are genetically identical. The source for the dataset is Laboratory of Genetics/NIA/NIH.
DOI: 10.6075/j0pg1qh8
title: CIL:26526, Mus musculus, fibroblast. In Cell Image Library

description: Cells were cultured in DME (Invitrogen) supplemented with 10% fetal bovine serum and 100 U/ml penicillin/streptomycin (Invitrogen) at 37°C in a humidified 5% CO2 incubator. Cells were fixed using 3.7% paraformaldehyde in PBS for 15 min, permeabilized using 0.2% Triton X-100 in PBS for 2 min, blocked with 2% BSA in PBS, and stained with the indicated primary antibodies for at 4°C overnight, followed by incubation with a secondary Alexa Fluor 488–, 546– or 594–conjugated antibody. Images were captured by Leica TCS SP2 confocal microscope with HCX PL APO 63X objective.
description: Preparation: formaldehyde fixed tissue; detergent permeabilized
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope
Visualization methods: Alexa Fluor 488; Alexa Fluor 546
Data qualification: Raw
description: To study the molecular mechanism by which nonmuscle myosin II (MII) regulates protrusion and adhesion dynamics in migrating cells, NIH3T3 cells were co-stained for βPIX (green) and myosin IIA (red). As a member of the Dbl family of Rho-GEFs (guanine nucleotide exchange factors), βPIX could contribute to cell motility through interactions with myosin. Findings from this study help elucidate a functional link between MII and Rac1/Cdc42 GTPases, which may regulate protrusion/adhesion dynamics in migrating cells. This image is original data from Fig. S2, "Colocalization of MII and GEFs in NIH3T3 fibroblasts," in J. Cell Biol. 2010. Vol. 190(4):663–674
DOI: 10.6075/j0jq0zsj
title: CIL:26529, Mus musculus, fibroblast. In Cell Image Library

description: To study the molecular mechanism by which nonmuscle myosin II (MII) regulates protrusion and adhesion dynamics in migrating cells, NIH3T3 cells were transfected with myc-tagged phosphomimetic constitutively active MLC mutants (MLCaa, green) and co-stained for TRIO (a multifunctional, multidomain Rho guanine nucleotide exchange factor, red) and filamentous actin (blue). These findings help elucidate a functional link between MII and Rac1/Cdc42 GTPases, which may regulate protrusion/adhesion dynamics in migrating cells. This image is the original data file from Fig. S5,"Expression of active MLC mutants inhibits the dissociation of MII–Trio complex," in J. Cell Biol. 2010. Vol. 190(4):663–674
description: Cells were cultured in DME (Invitrogen) supplemented with 10% fetal bovine serum and 100 U/ml penicillin/streptomycin (Invitrogen) at 37°C in a humidified 5% CO2 incubator. For transfections, cells in 60-mm-diameter dishes or on fibronectin-coated coverslips were incu- bated with a mixture of DNA and LipofectAMINE 2000 (Invitrogen) according to the manufacturer's instructions. The cDNA for MLC was subcloned into pCMV-myc (Takara Bio Inc.). Mutant constructs of MLC were generated using a QuikChange site-directed mutagenesis kit (Agilent Technologies) according to the manufacturer's protocol. In this myc-tagged MLC mutant, Ser1/Ser2 were replaced by alanines. In some experimental conditions, 16 h after replating onto fibronectin-coated coverslips, cells were treated with 50 ng/ml PDGF for 20 min. Cells were fixed 24–48 h after transfection using 3.7% paraformaldehyde in PBS for 15 min, permeabilized using 0.2% Triton X-100 in PBS for 2 min, blocked with 2% BSA in PBS, and co-stained for MLC (green), TRIO (red), and actin (blue). Images were captured by Zeiss LSM 710 confocal microscope with Plan-Apochromat 63X objective.
description: Preparation: formaldehyde fixed tissue; detergent permeabilized
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope; distribution of a specific protein
Visualization methods: Alexa Fluor 488; Alexa Fluor 546; phalloidin
Data qualification: Raw
DOI: 10.6075/j0ft8m7c
title: CIL:54914, Homo sapiens, pyramidal cell. In Cell Image Library

description: We examined the structural organization of cytoskeletal components and membrane systems in neurons of well preserved biopsy material from Alzheimer’s disease (AD). Information was obtained from thin sectioned material using conventional electron microscopy and from thick sections with the high voltage electron microscope.
description: This image displays the PHF array.
description: Imaging mode: Electronic tomography
DOI: 10.5281/zenodo.15873931
title: Supplementary dataset for "High-frequency monitoring reveals rainfall-driven phosphorus and nitrogen concentration–discharge patterns and associated mechanisms"

description: The repository contains the statistical data for 25 rainfall events, and all data necessary to reproduce the figures in the paper.
DOI: 10.5281/zenodo.15873932
title: Supplementary dataset for "High-frequency monitoring reveals rainfall-driven phosphorus and nitrogen concentration–discharge patterns and associated mechanisms"

description: The repository contains the statistical data for 25 rainfall events, and all data necessary to reproduce the figures in the paper.
DOI: 10.6075/j07p8zj9
title: CIL:40080, Rattus norvegicus, astrocyte, astrocyte of the hippocampus. In Cell Image Library

description: Intracellular injection of astrocytes in lightly fixed tissue slices was performed as previously described, with some modifications (Buhl et al., [1990], PMID: 2262598). The brain was placed in ice-cold PBS and cut into coronal slices with a vibratome at a thickness of 100 µm, and stored in PBS at 4°C until used. The slices were placed under a 60x water objective (NA 1.4) and observed with an Olympus BX50WI microscope using infrared-DIC optics (Olympus, Melville, NY). Astrocytes in the upper blade of the dentate gyrus were identified by the shape and size of their somata. Glass micropipettes (OD 1.00 mm, ID 0.58 mm; resistances 100-400 M) were pulled on a vertical puller (David Kopf Instruments, Tujunga, CA) and backfilled with Alexa 568. Astrocytes were impaled and iontophoretically injected with dye using 1-second pulses of negative current (0.5 Hz) for 1-2 minutes. After several cells were filled, the slices were placed in ice-cold 4% PFA for at least 1 hour. The slices were then ready to be immunolabeled. The rat anti-N-CAM monoclonal antibody (isoclone 12F11) was obtained from BD PharMingen (San Diego, CA), and detected using Alexa 488. Slices were coverslipped using Gelvatol (Harlow and Lane, [1988]) and allowed to set overnight at room temperature before they were examined.
Image acquisition and analysis: Specimens were examined using a Radiance2000 laser scanning confocal system (Bio-Rad, Hercules, CA) attached to a Nikon E600FN microscope (Kanagawa, Japan). A 60x oil immersion (NA 1.4) objective was used to image LY-filled astrocytes.
description: Projection through merged optical section series of a filled astrocyte (green) in the molecular layer of the dentate gyrus of a 1 month-old rat, stained for NCAM (red), showing the relationship between astrocyte processes and laminar boundaries revealed by NCAM staining. Optical sections were generated with a single photon confocal microscope. Original data contributed to Bushong EA, Martone ME, Ellisman MH. Examination of the relationship between astrocyte morphology and laminar boundaries in the molecular layer of adult dentate gyrus. J Comp Neurol. 2003 Jul 21;462(2):241-51. PMID: 12794746. This image has been downsampled from the raw data image which can be accessed using the link provided to the Cell Centered Database.
description: Preparation: formaldehyde fixed tissue
Relation to intact cell: vibratome-sectioned tissue
Item type: recorded image
Imaging mode: confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: intracellular filling; distribution of epitope
Visualization methods: Alexa Fluor 568; primary antibody plus labeled secondary antibody; Alexa Fluor 488
Data qualification: Processed
DOI: 10.6075/j0571b1c
title: CIL:7426, Homo sapiens, neuron. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue
Relation to intact cell: isolated subcellular component
Item type: recorded image
Imaging mode: microscopy; atomic force microscopy
Parameter imaged: specimen height
Source of contrast: specimen height
Processing history: Pixel value determine by specimen height
description: The protein MeCP2 binds to symmetrically methylated CpG dinucleotides and is thought to transmit the (generally) repressive signals encoded in DNA methylation patterns. Mutations in MeCP2 lead to Rett syndrome. Here, MeCP2-DNA complexes have been imaged by AFM (Digital Instruments Nanoscope) in air using human MeCP2 and an 828 bp DNA sequence containing several methylated CpGs. MeCP2, which appears as bright circles in AFM images, and volume measurements of the complexes suggest that MeCP2 monomers and dimers are present and that MeCP2 binds DNA cooperatively. Other images in the linked set show looped structures and large complexes containing multiple DNA strands and MeCP2 molecules. These configurations are likely promoted by the multiple independent DNA-binding domains of MeCP2.
DOI: 10.6075/j0sq908t
title: CIL: 54717. In Cell Image Library

description: Item type: EM tomogram
Imaging mode: Electronic tomography
description: We examined the structural organization of cytoskeletal components and membrane systems in neurons of well preserved biopsy material from Alzheimer’s disease (AD). Information was obtained from thin sectioned material using conventional electron microscopy and from thick sections with the high voltage electron microscope.
description: This image displays the PHF interacting with the nuclear envelope.
DOI: 10.6075/j0np23ww
title: CIL: 52149, Homo sapiens. In Cell Image Library

description: This assay utilizes physiological concentrations class I PI3Ka, 1mM ATP, drug identified in subfolder, and saturating concentrations of fluorescently-labeled GRP-PH domain, a PIP3 product lipid binder, in order to count each product lipid produced. Enzyme rates are calculated as the slope of product lipid created vs. time. 21.5 ± 0.5°C

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.
description: A single molecule TIRFM assay was employed to measure the kinase activity of purified PI3K molecules on a supported lipid bilayer by counting the number of product PIP3 molecules they produce.
description: Imaging mode: Fluoresence
Visualization methods: objective based TIRFM using a modified Nikon TE-2000U (60x 1.49 N.A. TIRF objective) and illumination from a 532-nm solid-state laser with power modification by neutral-density filters
DOI: 10.6075/j08052gx
title: CIL: 54667, Drosophila melanogaster, astrocytes (red). In Cell Image Library

description: Imaging mode: fluorescence microscopy
Visualization methods: Spinning Disk Confocal Imaging
description: Astrocyte-specific RFP expression was achieved using driven using the Gal4-UAS binary system and the driver alrm. Cortex-glia specific GFP was achieved using the lexA-lexAop binary system and the cortex-glia specific driver wrapper932i-LexA (Coutinho-Budd et al., 2017). The larval CNS was dissected in the third instar larval stage, fixed with methanol, stained for RFP, GFP and Elav (neuronal nuclei marker), and mounted in VectaShield reagent. Slides were imaged on an Innovative Imaging Innovations (3i) spinning disk confocal microscope equipped with a Yokogawa CSX-W1 using a 63X oil objective.

Staining: Astrocytes (red); Cortex glia (green); Neurons (blue)
description: Confocal image of the CNS of a D. melanogaster in the third instar larval stage after Spz3 KD, 0uM from the ventral surface, depicting astrocytes (red), cortex glia (green) and neuronal nuclei (blue). Our study examined the breakdown of the spatial segregation between cortex glia and astrocyte after disruption of cortex glial morphology. After knockdown of Spz3, a secreted neurotrophin, we observed aberrant infiltration by astrocytes into the cortex.
DOI: 10.6075/j0ht2nwn
title: CIL: 52587. In Cell Image Library

description: Tile x=1, y=6, z=16 from PS09_20676_2B_Myc_Terc
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: One z layer of a z-stack at the given tile position
DOI: 10.6075/j0n29x2h
title: CIL:38691, rat, Purkinje neuron. In Cell Image Library

description: Purkinje neuron from mouse cerebellum injected with Lucifer Yellow and imaged using confocal microscopy
description: Imaging mode: Optical section series