cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j03t9g8f
title: CIL:6562, Oryctolagus cuniculus, skeletal muscle cell. In Cell Image Library

description: Rabbit psoas skeletal muscle fibers were held at constant length and rigor induced by immersion in glycerol. The fibers were fixed in buffered glutaraldehyde, treated with tannic acid and quick-frozen by contact with a liquid helium-cooled copper block in a Heuser-type cryopress, and freeze-etched in a Balzers 400 freeze fracture machine. The sample was then rotary-replicated with Pt-C at 24 degrees and visualized in a JEOL 100CX2 transmission electron microscope operated at 100 kev.

This image was recorded on Kodak 4489 film at 75,000x magnification. Stereo pairs were taken at +5 and -5 degrees. Films were scanned with a 20 micrometer pixel spacing on a Nikon Coolscan 9000ED scanner.

Stereo pair with CIL:6563.
description: Preparation: glutaraldehyde fixed tissue; freeze_fracture/freeze_etch
Relation to intact cell: isolated subcellular component
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM); wide-field detection; widefield illumination; illumination by electrons; detection of electrons
Parameter imaged: electron density; elevation
Source of contrast: differences in deposition of metal shadow
Visualization methods: shadowing and plating
Processing history: unprocessed raw data
DOI: 10.6075/j0542mmn
title: CIL:6561, Oryctolagus cuniculus, skeletal muscle cell. In Cell Image Library

description: Rabbit psoas skeletal muscle fibers were held at constant length and rigor induced by immersion in glycerol. The fibers were fixed in buffered glutaraldehyde, treated with tannic acid and quick-frozen by contact with a liquid helium-cooled copper block in a Heuser-type cryopress, and freeze-etched in a Balzers 400 freeze fracture machine. The sample was then rotary-replicated with Pt-C at 24 degrees and visualized in a JEOL 100CX2 transmission electron microscope operated at 100 kev.

This image was recorded on Kodak 4489 film at 75,000x magnification. Stereo pairs were taken at +5 and -5 degrees. Films were scanned with a 20 micrometer pixel spacing on a Nikon Coolscan 9000ED scanner.

Stereo pair with CIL:6565.
description: Preparation: glutaraldehyde fixed tissue; freeze_fracture/freeze_etch
Relation to intact cell: isolated subcellular component
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM); wide-field detection; widefield illumination; illumination by electrons; detection of electrons
Parameter imaged: electron density; elevation
Source of contrast: differences in deposition of metal shadow
Visualization methods: shadowing and plating
Processing history: unprocessed raw data
DOI: 10.6075/j0ns0szb
title: CIL:6560, Oryctolagus cuniculus, skeletal muscle cell. In Cell Image Library

description: Rabbit psoas skeletal muscle fibers were held at constant length and rigor induced by immersion in glycerol. The fibers were fixed in buffered glutaraldehyde, treated with tannic acid and quick-frozen by contact with a liquid helium-cooled copper block in a Heuser-type cryopress, and freeze-etched in a Balzers 400 freeze fracture machine. The sample was then rotary-replicated with Pt-C at 24 degrees and visualized in a JEOL 100CX2 transmission electron microscope operated at 100 kev.

This image was recorded on Kodak 4489 film at 75,000x magnification. Stereo pairs were taken at +5 and -5 degrees. Films were scanned with a 20 micrometer pixel spacing on a Nikon Coolscan 9000ED scanner.

Stereo pair with CIL:6560.
description: Preparation: glutaraldehyde fixed tissue; freeze_fracture/freeze_etch
Relation to intact cell: isolated subcellular component
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM); wide-field detection; widefield illumination; illumination by electrons; detection of electrons
Parameter imaged: electron density; elevation
Source of contrast: differences in deposition of metal shadow
Visualization methods: shadowing and plating
Processing history: unprocessed raw data
DOI: 10.6075/j0hd7tq7
title: CIL:7105, Homo sapiens, neuron. In Cell Image Library

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 molecules appear as bright particles in AFM images. Volume measurements of the complexes suggest that MeCP2 monomers (circular particles) and dimers (larger elliptical particles) are present and suggest that MeCP2 binds DNA cooperatively. Other images in the grouped 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 and relevant to the in vivo interactions between MeCP2 and chromatin.
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: unprocessed raw data
DOI: 10.6075/j0cn72zf
title: CIL:7113, Homo sapiens, neuron. In Cell Image Library

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 molecules appear as bright particles in AFM images. Volume measurements of the complexes suggest that MeCP2 monomers (circular particles) and dimers (larger elliptical particles) are present and suggest that MeCP2 binds DNA cooperatively. Other images in the grouped 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 and relevant to the in vivo interactions between MeCP2 and chromatin.
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: unprocessed raw data
DOI: 10.15468/dl.fz8fnn
title: Occurrence Download

description: A dataset containing 30582 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Heracleum sosnowskyi"
 ]
}

 The dataset includes 30582 records from 66 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009699-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6075/j0vh5mxt
title: CIL:7103, Homo sapiens, neuron. In Cell Image Library

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 molecules appear as bright particles in AFM images. Volume measurements of the complexes suggest that MeCP2 monomers (circular particles) and dimers (larger elliptical particles) are present and suggest that MeCP2 binds DNA cooperatively. Other images in the grouped 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 and relevant to the in vivo interactions between MeCP2 and chromatin.
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: unprocessed raw data
DOI: 10.6075/j0ks6qk7
title: CIL:7101, 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: unprocessed raw data
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 molecules appear as bright particles in AFM images. Volume measurements of the complexes suggest that MeCP2 monomers (circular particles) and dimers (larger elliptical particles) are present and suggest that MeCP2 binds DNA cooperatively. Other images in the grouped 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 and relevant to the in vivo interactions between MeCP2 and chromatin.
DOI: 10.6075/j02z14th
title: CIL:696, Necturus maculosus, nucleate erythrocyte. In Cell Image Library

description: X-ray analysis shows that the nucleated erythrocytes of the amphibian Necturus maculosus (Mud Puppy) contains more ordered chromatin than most nuclei. Here, chromatin fibers were isolated from N. maculosus erythrocyte nuclei using mild micrococcal nuclease digestion, fixed briefly with glutaraldehyde, applied to thin carbon films and negatively stained with methylamine tungstate. ~30 nm fibers are seen, some exhibiting short regions with apparent structural order.
description: Preparation: unembedded tissue; glutaraldehyde fixed tissue
Relation to intact cell: isolated subcellular component
Item type: transmission electron microscopy (TEM)
Imaging mode: illumination by electrons; detection of electrons
Parameter imaged: electron density
Source of contrast: elastic scattering
Visualization methods: other negative stain
Processing history: raw unprocessed data
DOI: 10.6075/j08s4p4f
title: CIL:695, Necturus maculosus, nucleate erythrocyte. In Cell Image Library

description: Preparation: unembedded tissue; glutaraldehyde fixed tissue
Relation to intact cell: isolated subcellular component
Item type: transmission electron microscopy (TEM)
Imaging mode: illumination by electrons; detection of electrons
Parameter imaged: electron density
Source of contrast: elastic scattering
Visualization methods: other negative stain
Processing history: raw unprocessed data
description: X-ray analysis shows that the nucleated erythrocytes of the amphibian Necturus maculosus (Mud Puppy) contains more ordered chromatin than most nuclei. Here, chromatin fibers were isolated from N. maculosus erythrocyte nuclei using mild micrococcal nuclease digestion, fixed briefly with glutaraldehyde, applied to thin carbon films and negatively stained with methylamine tungstate. ~30 nm fibers are seen, some exhibiting short regions with apparent structural order.
DOI: 10.6075/j0571b9z
title: CIL:688, Zea mays, photosynthetic cell. In Cell Image Library

description: The plastids of plants germinated in the dark are termed etioplasts and possess quasi-crystalline structures termed prolammelar bodies that contain the phospholipid materials and chlorophyll precursors that are converted to green chloroplasts in response to light. The micrograph shows a corn (Zea mays) etioplast fixed after brief exposure to light. The prolamellar body has largely been transformed into thylakoid membranes that are starting to assume their mature stacked conformation. Other images in this group show the prolamellar body.
description: Preparation: glutaraldehyde fixed tissue; tissue in plastic embedment; osmium tetroxide fixed tissue
Relation to intact cell: microtome-sectioned tissue
Item type: film
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: uranyl salt; osmium tetroxide; lead salt
Processing history: raw unprocessed image
description: Zea mays seeds were germinated in the dark, briefly exposed to light, and segments of coleoptile, excised, fixed with glutataldehyde, post-fixed with osmuim tetroxide, and embedded in epoxy resin. Thin sections were cut, stained with uranyl acetate and lead citrate, and observed using a Philips 300 transmission EM. Images were recorded on film.
DOI: 10.6075/j0xg9qd4
title: CIL:687, Zea mays, photosynthetic cell. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue; tissue in plastic embedment; osmium tetroxide fixed tissue
Relation to intact cell: microtome-sectioned tissue
Item type: film
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: uranyl salt; osmium tetroxide; lead salt
Processing history: raw unprocessed image
description: Zea mays seeds were germinated in the dark, briefly exposed to light, and segments of coleoptile, excised, fixed with glutataldehyde, post-fixed with osmuim tetroxide, and embedded in epoxy resin. Thin sections were cut, stained with uranyl acetate and lead citrate, and observed using a Philips 300 transmission EM. Images were recorded on film.
description: The plastids of plants germinated in the dark are termed etioplasts and possess quasi-crystalline structures termed prolammelar bodies that contain the phospholipid materials and chlorophyll precursors that are converted to green chloroplasts in response to light. The micrograph shows a corn (Zea mays) etioplast fixed after brief exposure to light. Te residual prolamellar body is not seen in this section, but, but thylakoid membranes are starting to form and stack. Other images in this group show the prolamellar body.
DOI: 10.6075/j0rb73xq
title: CIL:684, Zea mays, photosynthetic cell. In Cell Image Library

description: The plastids of plants germinated in the dark are termed etioplasts and possess quasi-crystalline structures termed prolammelar bodies that contain the phospholipid materials and chlorophyll precursors that are converted to green chloroplasts in response to light. The micrograph shows a corn (Zea mays) etioplast fixed after brief exposure to light. The prolamellar body is still largely intact, but thylakoid membranes are starting to form.
description: Zea mays seeds were germinated in the dark, briefly exposed to light, and segments of coleoptile, excised, fixed with glutataldehyde, post-fixed with osmuim tetroxide, and embedded in epoxy resin. Thin sections were cut, stained with uranyl acetate and lead citrate, and observed using a Philips 300 transmission EM. Images were recorded on film.
description: Preparation: glutaraldehyde fixed tissue; tissue in plastic embedment; osmium tetroxide fixed tissue
Relation to intact cell: microtome-sectioned tissue
Item type: film
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: uranyl salt; osmium tetroxide; lead salt
Processing history: raw unprocessed image
DOI: 10.6075/j05q4v5b
title: CIL:6566, Oryctolagus cuniculus, skeletal muscle cell. In Cell Image Library

description: Rabbit psoas skeletal muscle fibers were held at constant length and rigor induced by immersion in glycerol. The fibers were fixed in buffered glutaraldehyde, treated with tannic acid and quick-frozen by contact with a liquid helium-cooled copper block in a Heuser-type cryopress, and freeze-etched in a Balzers 400 freeze fracture machine. The sample was then rotary-replicated with Pt-C at 24 degrees and visualized in a JEOL 100CX2 transmission electron microscope operated at 100 kev.

This image was recorded on Kodak 4489 film at 75,000x magnification. Stereo pairs were taken at +5 and -5 degrees. Films were scanned with a 20 micrometer pixel spacing on a Nikon Coolscan 9000ED scanner.

Stereo pair with CIL:6558.
description: Preparation: glutaraldehyde fixed tissue; freeze_fracture/freeze_etch
Relation to intact cell: isolated subcellular component
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM); wide-field detection; widefield illumination; illumination by electrons; detection of electrons
Parameter imaged: electron density; elevation
Source of contrast: differences in deposition of metal shadow
Visualization methods: shadowing and plating
Processing history: unprocessed raw data
DOI: 10.5281/zenodo.17492646
title: TDN in the repair of urethral injury in rats

description: This deposit contains the processed RNA-seq data and documentation for the study ‘TDN in the repair of urethral injury in rats’. Total RNA was extracted from rat urethral tissues across four groups (control, model, model + rapamycin, model + TDN). Sequencing was performed on Illumina NovaSeq 6000 (PE150). Clean reads were aligned to the rat reference genome (Rnor_6.0). Differential expression was analyzed (e.g., DESeq2); enrichment (GO/KEGG/Reactome/ssGSEA) was performed in R. Processed matrices and DEG tables are provided; raw FASTQ will be deposited to SRA/GEO as required by journal policy.
DOI: 10.5281/zenodo.17492647
title: TDN in the repair of urethral injury in rats

description: This deposit contains the processed RNA-seq data and documentation for the study ‘TDN in the repair of urethral injury in rats’. Total RNA was extracted from rat urethral tissues across four groups (control, model, model + rapamycin, model + TDN). Sequencing was performed on Illumina NovaSeq 6000 (PE150). Clean reads were aligned to the rat reference genome (Rnor_6.0). Differential expression was analyzed (e.g., DESeq2); enrichment (GO/KEGG/Reactome/ssGSEA) was performed in R. Processed matrices and DEG tables are provided; raw FASTQ will be deposited to SRA/GEO as required by journal policy.
DOI: 10.6075/j0cj8ckk
title: CIL:6565, Oryctolagus cuniculus, skeletal muscle cell. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue; freeze_fracture/freeze_etch
Relation to intact cell: isolated subcellular component
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM); wide-field detection; widefield illumination; illumination by electrons; detection of electrons
Parameter imaged: electron density; elevation
Source of contrast: differences in deposition of metal shadow
Visualization methods: shadowing and plating
Processing history: unprocessed raw data
description: Rabbit psoas skeletal muscle fibers were held at constant length and rigor induced by immersion in glycerol. The fibers were fixed in buffered glutaraldehyde, treated with tannic acid and quick-frozen by contact with a liquid helium-cooled copper block in a Heuser-type cryopress, and freeze-etched in a Balzers 400 freeze fracture machine. The sample was then rotary-replicated with Pt-C at 24 degrees and visualized in a JEOL 100CX2 transmission electron microscope operated at 100 kev.

This image was recorded on Kodak 4489 film at 75,000x magnification. Stereo pairs were taken at +5 and -5 degrees. Films were scanned with a 20 micrometer pixel spacing on a Nikon Coolscan 9000ED scanner.

Stereo pair with CIL:6561.
DOI: 10.6075/j0q52nnt
title: CIL:6564, Oryctolagus cuniculus, skeletal muscle cell. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue; freeze_fracture/freeze_etch
Relation to intact cell: isolated subcellular component
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM); wide-field detection; widefield illumination; illumination by electrons; detection of electrons
Parameter imaged: electron density; elevation
Source of contrast: differences in deposition of metal shadow
Visualization methods: shadowing and plating
Processing history: unprocessed raw data
description: Rabbit psoas skeletal muscle fibers were held at constant length and rigor induced by immersion in glycerol. The fibers were fixed in buffered glutaraldehyde, treated with tannic acid and quick-frozen by contact with a liquid helium-cooled copper block in a Heuser-type cryopress, and freeze-etched in a Balzers 400 freeze fracture machine. The sample was then rotary-replicated with Pt-C at 24 degrees and visualized in a JEOL 100CX2 transmission electron microscope operated at 100 kev.

This image was recorded on Kodak 4489 film at 75,000x magnification. Stereo pairs were taken at +5 and -5 degrees. Films were scanned with a 20 micrometer pixel spacing on a Nikon Coolscan 9000ED scanner.

Stereo pair with CIL:6567.
DOI: 10.6075/j0ws8sg8
title: CIL:710, Gallus gallus, nucleate erythrocyte. In Cell Image Library

description: chicken erythrocyte nuclei were allowed to decondense in a low salt high pH buffer, fixed with HCOH, centrifuged onto a carbon coated EM grid, and stained with uranyl acetate. (Spreading technique of Oscar L Miller Jr).
 Beaded chains of nucleosomes separated by linker DNA are seen emanating from a central mass of less dispersed chromatin.
description: Preparation: formaldehyde fixed tissue
Relation to intact cell: isolated subcellular component
Item type: transmission electron microscopy (TEM)
Imaging mode: illumination by electrons
Parameter imaged: electron density
Source of contrast: elastic scattering
Visualization methods: visualization of contiguous regions; uranyl salt
Processing history: unprocessed raw data
DOI: 10.6075/j0hh6j3h
title: CIL:7102, Homo sapiens, neuron. In Cell Image Library

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 molecules appear as bright particles in AFM images. Volume measurements of the complexes suggest that MeCP2 monomers (circular particles) and dimers (larger elliptical particles) are present and suggest that MeCP2 binds DNA cooperatively. Other images in the grouped 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 and relevant to the in vivo interactions between MeCP2 and chromatin.
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: unprocessed raw data