cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j00c4tjv
title: CIL:13588, Mus musculus, myoblast. In Cell Image Library

description: The image was taken by leica DMI 4000B microscope equipped with a QImaging RETIGA Exi camera and Leica 10X/0.22 lens. 

Myosin heavy chain (MHC) expressed in myotubes was labeled by MF-20 mouse antibody followed by FITC-anti-mouse IgG secondary antibody. Nuclei were stained by DAPI. MHC and nuclei were pseudocolored in green and blue, respectively.
description: The C2C12 cell line, a mouse myoblast line, was used here to study the regulatory factors in myogenic differentiation. After cultured in differentiation medium for 3 days, these cells differentiated into myotubes (Green) containing multiple nuclei (Blue). The myoblasts in this image were transfected with the locked nucleic acid (LNA) anti-miR-1. During the last 2 days of differentiation, cells were treated with 0.2ug/ml recombinant follistatin. The effect of miR-1 was rescued by follistatin.

This image is the control of different treatments in Figure 6B from JCB 189: 1157-1169, 2010. See also CIL: 13585, 13586, 13587.
description: Preparation: formaldehyde fixed tissue; permeabilized tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: compartmentalization of stain or label; distribution of epitope
Visualization methods: Fluorescein (FITC); 4',6-diamidino-2-phenylindole (DAPI); primary antibody plus labeled secondary antibody
Processing history: brightness and contrast adjusted
Data qualification: Processed;spatialmeasurements;intensitiesquantitation
DOI: 10.6075/j05h7f06
title: CIL:13656, Homo sapiens, epithelial cell, cervical carcinoma. In Cell Image Library

description: HeLa cells transiently expressing GlcNAcT-1-HA-KDEL were fixed, immunolabeled for GlcNAcT-1-HA-KDEL (red) and endogenous alpha-mannosidase II (ManII, green), and examined by fluorescence microscopy. Endogenous ManII displayed different staining patterns, depending upon the level of expression of GlcNAcT-1-HA-KDEL. In this image, ManII is localized to the Golgi. Other images in Fig 6 show ManII localization to the ER (CIL# 13655), or cells in which ManII protein is lost completely (CIL# 13657). Transfected HeLa cells were fixed in 3% paraformaldehyde, blocked with 0.2% Triton X-100, 1% FBS, 0.5% BSA in PBS with Ca[2+] and Mg[2+], followed by incubation in primary antibodies (anti–human ManII rabbit pAb and anti-HA mouse mAb, HA.11 (Covance)) and secondary antibodies (Alexa 568 and Alexa 488) and DAPI (blue) to stain nuclei. Cells were mounted using Fluoromount (SouthernBiotech). Immunofluorescent images were digitally acquired on an inverted microscope (Axiovert 200M; Carl Zeiss, Inc.) coupled to a 12-bit cooled charge-coupled device camera (AxioCam MRm Rev. 3; Carl Zeiss, Inc.) controlled by Axiovision software (AxioVs40, version 4.7.2.0; Carl Zeiss, Inc.), using a 100x/1.3 NA oil immersion objective (EC Plan-NeoFluar; Carl Zeiss, Inc.), and saved as tiff files (1388 × 1040, 8 bit). All pictures were treated identically using Adobe Photoshop to remove background and adjust contrast. This image corresponds to Figure 6D, middle panel (merge) in J Cell Biol. 190: 893-910, 2010. Images in Fig 6 include CIL#s 13655, 13656, 13657.
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 a specific protein; compartmentalization of stain or label
Visualization methods: Alexa Fluor 488; Alexa Fluor 568; 4',6-diamidino-2-phenylindole (DAPI); primary antibody plus labeled secondary antibody; HA peptide tag
Data qualification: Processed;spatialmeasurements
DOI: 10.5281/zenodo.17490787
title: Demo Dataset for Deep Learning Accelerated First-Principles Quantum Transport Simulations at Nonequilibrium State
DOI: 10.5281/zenodo.17490788
title: Demo Dataset for Deep Learning Accelerated First-Principles Quantum Transport Simulations at Nonequilibrium State
DOI: 10.6075/j04x56h3
title: CIL:13658, Homo sapiens, epithelial cell, cervical carcinoma. In Cell Image Library

description: A major proportion of the medial-golgi enzyme tagged with HA, GlcNAcT-1-HA (green), is mislocalized to the ER when coexpressed with Myc-GnT1IP-L (Myc-tagged GlcNAcT-1 inhibitory protein, long transcript, membrane-anchored) (red). Transiently expressed Myc-GnT1IP-L itself is normally primarily localized in the Golgi and ERGIC and partially in the ER (shown in Fig 4; J Cell Biol. 190: 893-910, 2010.). Transfected HeLa cells were fixed in 3% paraformaldehyde, blocked with 0.2% Triton X-100, 1% FBS, 0.5% BSA in PBS with Ca[2+] and Mg[2+], followed by incubation in primary antibodies (anti-Myc mouse mAB, 9E10 (Covance) and anti-HA mouse mAb, HA.11 (Covance) and secondary antibodies (Alexa 568 and Alexa 488) and DAPI (blue) to stain nuclei. Cells were mounted using Fluoromount (SouthernBiotech). Images of confocal microscopy were acquired by capturing Z-series images with a 0.25-µm step size on a confocal microscope (TCS SP2 AOBS; Leica) using a 63x/1.4 NA oil immersion objective (HCX PL APO λBL CS; Leica). Laser lines at 405-, 488-, and 561-nm were provided by 20 mW diode, 100 mW Ar, and 10 mW diode, respectively; sequential excitation by line and detection range settings was used to eliminate cross talk between fluorophores. The images (512 × 512 pixel, 8 bit) were saved as tiff files. The entire Z-series was projected using the sum intensity method provided by ImageJ (NIH). This image corresponds to Figure 5A, top panel (merge) in J Cell Biol. 190: 893-910, 2010. Images in Fig 5 include CIL#s 13658, 24919, 24920.
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 emission
Source of contrast: distribution of a specific protein; compartmentalization of stain or label
Visualization methods: Alexa Fluor 488; Alexa Fluor 568; 4',6-diamidino-2-phenylindole (DAPI); primary antibody plus labeled secondary antibody; c-MYC peptide tag; HA peptide tag
Data qualification: Raw;spatialmeasurements
DOI: 10.6075/j0qn65kg
title: CIL:41655, Vorticella. In Cell Image Library

description: Preparation: living tissue
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
description: Video showing Vorticella (bell-shaped protozoans), ciliates attached to filamentous alga. The myoneme within the stalks contract with one of the fastest known movements in nature. Images were collected using differential interference contrast microscopy at 60X. Honorable Mention, 2011 Olympus BioScapes Digital Imaging Competition©.
DOI: 10.6075/j07p8x4h
title: CIL:13655, Homo sapiens, epithelial cell, cervical carcinoma. In Cell Image Library

description: HeLa cells transiently expressing GlcNAcT-1-HA-KDEL were fixed, immunolabeled for GlcNAcT-1-HA-KDEL (red) and endogenous alpha-mannosidase II (ManII, green), and examined by fluorescence microscopy. Endogenous ManII displayed different staining patterns, depending upon the level of expression of GlcNAcT-1-HA-KDEL. In this image, ManII is mislocalized to the ER. Other images in Fig 6 show ManII localization to the Golgi (CIL# 13656), or cells in which ManII protein is lost completely (CIL# 13657). Transfected HeLa cells were fixed in 3% paraformaldehyde, blocked with 0.2% Triton X-100, 1% FBS, 0.5% BSA in PBS with Ca[2+] and Mg[2+], followed by incubation in primary antibodies (anti–human ManII rabbit pAb and anti-HA mouse mAb, HA.11 (Covance)) and secondary antibodies (Alexa 568 and Alexa 488) and DAPI (blue) to stain nuclei. Cells were mounted using Fluoromount (SouthernBiotech). Immunofluorescent images were digitally acquired on an inverted microscope (Axiovert 200M; Carl Zeiss, Inc.) coupled to a 12-bit cooled charge-coupled device camera (AxioCam MRm Rev. 3; Carl Zeiss, Inc.) controlled by Axiovision software (AxioVs40, version 4.7.2.0; Carl Zeiss, Inc.), using a 100x/1.3 NA oil immersion objective (EC Plan-NeoFluar; Carl Zeiss, Inc.), and saved as tiff files (1388 × 1040, 8 bit). All pictures were treated identically using Adobe Photoshop to remove background and adjust contrast. This image corresponds to Figure 6D, top panel (merge) in J Cell Biol. 190: 893-910, 2010. Images in Fig 6 include CIL#s 13655, 13656, 13657.
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 a specific protein; compartmentalization of stain or label
Visualization methods: Alexa Fluor 488; Alexa Fluor 568; 4',6-diamidino-2-phenylindole (DAPI); primary antibody plus labeled secondary antibody; HA peptide tag
Data qualification: Processed;spatialmeasurements
DOI: 10.6075/j09g5khq
title: CIL:13654, Homo sapiens. In Cell Image Library

description: Preparation: formaldehyde fixed tissue
Relation to intact cell: whole mounted tissue
Item type: confocal microscopy; bright-field microscopy
Imaging mode: confocal microscopy; bright-field microscopy
Parameter imaged: fluorescence emission; optical path length gradient
Source of contrast: distribution of a specific protein; boundaries between regions with different refractive index
Visualization methods: Green fluorescent proteins from Aequorea; mCherryFP
Data qualification: Raw
description: Image is Fig. 4D in PMID: 20679433. HeLa cells were transfected to co-express p125A-mCherry and Sec31A-GFP. p125A colocalizes extensively with Sec31A; live cell time-lapse video microscopy showed that p125A (red) and Sec31A (green) positive structures are colocalized stably with each other over time, and undergo homotypic fusion. The vesicular structures of p125A-mCherry colocalize extensively with those of Sec31A-GFP over a period of at least 30 min. Cells were cultured on glass-bottom culture dishes, transfected with plasmid constructs of interest, and imaged using the Olympus Fluoview 1000 confocal microscope. 60X objective.
DOI: 10.6075/j03r0rm4
title: CIL:13652, Homo sapiens. In Cell Image Library

description: Preparation: formaldehyde fixed tissue
Relation to intact cell: whole mounted tissue
Item type: fluorescence microscopy
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: GFP
Data qualification: Raw
description: This image is fig. 6B in PMID:20679433. Exogenous expression of myc-p125A can rescue the dispersed Golgi phenotype in p125A depleted cells. HeLa cells stably expressing GT-GFP were transfected twice with ON-Targetplus SMARTpool siRNA (Dharmacon) against p125A with a 24 hour interval. 48 hour after siRNA transfection, the cells were transfected again to express myc-p125A. At 72 hour after the initial siRNA transfection, the cells were processed for indirect imunofluosecence microscopy to view GT-GFP (green) and myc-p125A (secondary Ab: goat anti-Rabbit Ab labeled with Alexa 555, pseudocolor in red).

Technical details: Cells grown on coverslips were washed 2X with PBS supplemented with 1 mM CaCl2 and 1 mM MgCl2 (PBSCM), fixed with 4% paraformaldehyde in PBSCM for 20 min at RT, washed 5X at 5-min intervals using PBSCM, and then permeabilized with 0.1% Saponin in PBSCM for 20 min at RT. The cells were then immunolabeled with appropriate primary antibodies diluted in fluorescence dilution buffer (FDB; PBSCM with 5% FBS and 2% bovine serum albumin [BSA]) for 1 h at RT, washed 5X with 0.1% Saponin PBSCM at 5-min intervals. Secondary antibodies were diluted in FDB and incubated at RT for 1 h, washed again with 0.1% Saponin PBSCM 5X at 5-min intervals, and then 2X with PBSCM. The coverslips were mounted on microscopic slides with Vectashield mounting medium containing DAPI. Confocal microscopy was performed with an Axioplan II microscope (Carl Zeiss, Inc.) equipped with Zeiss confocal scanning optics.
DOI: 10.6075/j0c53kg1
title: CIL: 53440, 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: CAMK 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/j0kw5f1d
title: CIL:36473, Xenopus laevis, fertilized egg. In Cell Image Library

description: Preparation: methanol fixed tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: single-spot confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope; distribution of a specific protein
Visualization methods: labeled primary antibody
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: This image is part of a large data set of Xenopus laevis eggs imaged at various times post fertilization (the first number of the file name corresponds minutes, eg 30_2 is 30 min post fertilization). The embryos are stained for alpha-tubulin (green) using a directly labeled B-5-1-2 antibody and DNA (red).
description: Images collected on a Zeiss LSM 710 confocal with a 10X 0.3 NA objective using 561 and 633 laser lines.
DOI: 10.6075/j0jq0zvf
title: CIL:13523, Mus musculus, neuronal stem cell. In Cell Image Library

description: Preparation: formaldehyde fixed tissue; permeabilized tissue
Relation to intact cell: microtome-sectioned tissue
Item type: recorded image
Imaging mode: spinning disk confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: differences in adsorption or binding of stain; distribution of epitope; distribution of a specific protein
Visualization methods: Alexa Fluor 488; 4',6-diamidino-2-phenylindole (DAPI); Alexa Fluor 568
Data qualification: Raw
description: A confocal Z-stack of neurons in postnatal hippocampus, expressing a GFP-tagged knockdown construct for the microRNA miR-137 (green, sh-miR-137) and immunostained to localize doublecortin (red), a marker of neuronal differentiation, and labeled with Dapi (blue), to determine the function of this microRNA in vivo. miR-137 regulates a core transcription factor in stem cell renewal, and data from these experiments suggest that high levels of miR-137promotes neuronal stem cell proliferation, but repressed neuronal differentiation. This image is original data from Fig. 5 of Szulwach et al.(2010) Cross talk between microRNA and epigenetic regulation in adult neurogenesis, J. Cell Biol. Vol. 189:127–141.
description: A retroviral vector containing sh-miR-137 under a U6 promoter and EGFP under a chicken actin promoter was prepared, and the virus containing the construct was injected into the dentate gyrus of adult mice in vivo. After 1 week, animals were anesthetized, perfused with 4% paraformaldehyde, brains removed and postfixed, equilibrated in 30% sucrose, and sectioned at a thickness of 40µm with a sliding microtome. Infected cells were localized using chicken-α-GFP (Invitrogen) and rabbit-α-DCX (Cell Signaling Technology), secondaries were α-chicken Alexa Fluor 488 and goat-α-rabbit Alexa Fluor 568 (both from Invitrogen). Confocal z-stacks were acquired at 1 µm steps using a Nikon TE2000 with equipped with a spinning disc confocal with an oil immersion 40X 1.3 NA objective (Zeiss). For additional details see: J. Cell Biol. Vol. 189:127–141.
DOI: 10.6075/j0wh2nr5
title: CIL:13487, Saccharomyces cerevisiae. In Cell Image Library

description: PrA contains a distinct determinant for glycan-independent ERAD (ER associated degradation). A mutant of the vacuolar proteinase A (PrA*-Gldelta4) (green) is a substrate of ER quality control (ERQC) mechanisms, as determined by the fact that it is retained in the ER (marked by Kar2; red), but is incompetent for ERAD. S. cerevisiae wild-type bearing PrA*-Gldelt4-HA centromeric plasmid were fixed in 3.7% formaldehyde. The cell wall was removed by zymolyase digestion in 1.2M sorbitol and washed resuspended cells were applied to poly L-lysine coated slide, methanol (-20C) and acetone treated, and air dried. Primary antibodies HA.11 mAb (Covance) and polyclonal rabbit anti-Kar2p were applied in 0.05% Tween 20 followed by Alexa Fluor 488 goat anti–mouse and Alexa Fluor 594 goat anti–rabbit (Invitrogen) secondary antibodies. Slides were mounted in PBS, 90% glycerol and DAPI (blue). Cells were visualized using an inverted microscope (LSM 510 META; Carl Zeiss, Inc.) with a Plan Apochromat 100× 1.4 NA Ph3 objective (Carl Zeiss, Inc.) in immersion oil (Immersol 518F; Carl Zeiss, Inc.) at room temperature. Image acquisition was performed using standard photomultiplier tube with LSM 510. Images were archived using LSM 5 Image Examiner (Carl Zeiss, Inc.) and Photoshop (version 7.0; Adobe), and no additional software adjustments were performed on images after acquisition other than cropping. Image corresponds to Fig 5D in J Cell Biol. 2010. 188:707-716.
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 emission
Source of contrast: distribution of a specific protein; compartmentalization of stain or label
Visualization methods: HA peptide tag; primary antibody plus labeled secondary antibody; 4',6-diamidino-2-phenylindole (DAPI); Alexa Fluor 488; Alexa Fluor 594
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
DOI: 10.6075/j02f7m2j
title: CIL:13486, Saccharomyces cerevisiae. In Cell Image Library

description: A mutant of the vacuolar proteinase A (ngPrAdelta295-331) (green) is a substrate of ER quality control (ERQC) mechanisms, as determined by the fact that it is retained in the ER (marked by Kar2; red) when degradation is blocked through deletion mutation of hrd1. S. cerevisiae mutant hrd1::KANMX (deletion mutation of hrd1) bearing ngPRdelta295-331-HA centromeric plasmid were fixed in 3.7% formaldehyde. The cell wall was removed by zymolyase digestion in 1.2M sorbitol and washed resuspended cells were applied to poly L-lysine coated slide, methanol (-20C) and acetone treated, and air dried. Primary antibodies HA.11 mAb (Covance) and polyclonal rabbit anti-Kar2p were applied in 0.05% Tween 20 followed by Alexa Fluor 488 goat anti–mouse and Alexa Fluor 594 goat anti–rabbit (Invitrogen) secondary antibodies. Slides were mounted in PBS, 90% glycerol and DAPI (blue). Cells were visualized using an inverted microscope (LSM 510 META; Carl Zeiss, Inc.) with a Plan Apochromat 100× 1.4 NA Ph3 objective (Carl Zeiss, Inc.) in immersion oil (Immersol 518F; Carl Zeiss, Inc.) at room temperature. Image acquisition was performed using standard photomultiplier tube with LSM 510. Images were archived using LSM 5 Image Examiner (Carl Zeiss, Inc.) and Photoshop (version 7.0; Adobe), and no additional software adjustments were performed on images after acquisition other than cropping. Image corresponds to Fig 1D in J Cell Biol. 2010. 188:707-716.
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 emission
Source of contrast: compartmentalization of stain or label; distribution of a specific protein
Visualization methods: HA peptide tag; primary antibody plus labeled secondary antibody; 4',6-diamidino-2-phenylindole (DAPI); Alexa Fluor 488; Alexa Fluor 594
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
DOI: 10.6075/j0m04440
title: CIL:13676, Drosophila melanogaster, motor neuron. In Cell Image Library

description: Preparation: formaldehyde fixed tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: spinning disk confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: primary antibody plus labeled secondary antibody; beta-galactosidase; Alexa Fluor 488; Cy3
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: The JNK phosphatase puckered, whose expression can be reported via a lacZ enhancer trap, is expressed in very low levels in uninjured neurons; however, nerve crush induces a dramatic increase in puc-lacZ expression in injured motoneurons. This image stack shows puc-lacZ (green) and neuronal nuclei (red) in a third instar larva injured at site 2 (as defined in Fig 1C). Wandering third instar larvae were dissected in PBS and fixed in either 4% paraformaldehyde in PBS or Bouin's fixative for 15–30 min. Primary antibodies used were: rat anti-elaV (7E8A10, Developmental Studies Hybridoma Bank) and mouse anti-lacZ (40-1a, DSHB). Secondary antibodies were Alexa 488 anti-mouse and Cy3 anti-rat. Confocal images were collected at room temperature on a spinning-disk confocal system (PerkinElmer) consisting of a scanner (Nipkow CSU10; Yokogawa) and an electron microscopy charge-coupled device camera (C9100-50; Hamamatsu Photonics) mounted on an inverted microscope (Axio Observer; Carl Zeiss, Inc.) with 25× 0.8 NA multi and 40× 1.3 NA, 63× 1.5 NA, and 100× 1.46 NA oil objectives. Similar settings were used to collect all compared genotypes. All imaging and quantification were conducted with Volocity software (PerkinElmer). This image stack corresponds to Fig 1E2 in J Cell Biol. 2010. 191: 211-223. Images in Fig 1 include CIL#s 13676, 13677, 13678, 13679.