cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0br8rh0
title: CIL:41607, Cricetulus griseus, epithelial cell, ovary. In Cell Image Library

description: Preparation: chemically fixed tissue
Relation to intact cell: squash preparation
Item type: film
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: uranyl salt
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: CHO cells arrested at metaphase with colcemid were treated with 67% D2O, in 0.07M phosphate buffer and squashed in 50% acetic acid. Preparations were transferred to EM grids and examined with the Wisconsin HVEM operated at 1MeV.
See also: H. Ris 1981 Stereoscopic electron microscopy of chromosomes. Meth Cell Biol 22:77-96 H. Ris 1978 Preparation of chromatin and chromosomes for electron microscopy. Meth Cell Biol 18:220-246.
description: High Voltage Transmission EM of whole mitotic metaphase chromosomes from Chinese hamster ovary cells. This image was recorded at a specimen tilt of 49 degrees and is grouped with one taken at 55 degrees, creating a stereo pair giving an oblique 3D view of the chromosomes.
DOI: 10.6075/j0q52nkx
title: CIL:35563, Rattus rattus, duct epithelial cell, hepatocyte. In Cell Image Library

description: Preparation: cryofixed tissue; chemically fixed tissue; phalloidin; primary antibody plus labeled secondary antibody
Relation to intact cell: sectioned tissue
Item type: recorded image
Imaging mode: single point scanning
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: Cy5; Cy3; Fluorescein (FITC)
Processing history: channels merged
Data qualification: Processed;spatialmeasurements
description: Liver of a rat exposed to chemical carcinogens. Serial sections of the liver imaged by laser scanning confocal microscopy. F-actin (red) is in bile canaliculi at junctions of the hepatocytes, which are the large round cells arranged in a circular mass in the bottom center, in ductule cells, which are above and to the left of the hepatocytes, and in blood vessel endothelial cells, which are in the upper right and far left. Fibronectin (green) is in the tissue outside the hepatocytes. Bile ductule and/or oval cells are marked blue.
description: The liver of a rat fed a carcinogenic chemicals diet was cryo- and paraformaldehyde-fixed and frozen sections were prepared. The section was labeled with Cy 3 for OV-6, a marker for oval cells/bile ductile cells, Cy5 for fibronectin, and FITC for f-actin. Colors in this image were assigned to each probe by the Cell Imaging Library software. The confocal microscope was a BioRad MRC 600 with a Kr/Ar laser with lines at 488, 568, and 647 nm mounted on a Nikon Diaphot with 60X N.A. 1.4 phase 3 optics. Because the scan head only had two photomultiplier tubes, the filters had to be swapped out manually to collect a series of in register images of more than two fluorescent probes. The microscope was in the Analytical Imaging Facility of the Albert Einstein College of Medicine.
DOI: 10.6075/j0t43rrc
title: CIL:37125, Mus musculus, endothelial cell. In Cell Image Library

description: Transmission electron micrograph showing capillary mouse myocardium continuous endothelium using a hemoglobin tracer in caveolae. Hemoglobin, used as a tracer, is seen in the lumen of a capillary lined by a continuous endothelium, in endothelial caveolae, and in the extracellular space. Tracers such as hemoglobin or small heme-peptides were used by these investigators to demonstrate the role of caveolae in transcytosis of molecules across continuous capillary endothelial cells. Image made available by James D. Jamieson and the Department of Cell Biology, Yale University School of Medicine.
description: Reference:
Simeonescu, N., M. Simeonescu, and G. E. Palade. 1975. J. Cell Biol. 64:586-607.

Original 3.25 in. x 4 in. lantern slides were scanned at 600dpi. Original magnification X84,000.
description: Preparation: glutaraldehyde fixed tissue; formaldehyde fixed tissue; Graham-Karnosky method; digallic acid
Relation to intact cell: sectioned tissue
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: osmium tetroxide
DOI: 10.6075/j0s181w1
title: CIL:41453, Cricetulus griseus, epithelial cell. In Cell Image Library

description: Preparation: formaldehyde fixed tissue; tissue in plastic embedment
Relation to intact cell: microtome-sectioned tissue
Item type: film
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: uranyl salt
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: CHO cells at metaphase were fixed with paraformaldehyde followed by OsO4, embedded in epoxy resin and 0.5 micrometer 'thick' sections stained with uranly acetate for HVEM observation.
See also:
H. Ris 1981 Stereoscopic electron microscopy of chromosomes. Meth Cell Biol 22:77-96
H. Ris 1978 Preparation of chromatin and chromosomes for electron microscopy. Meth Cell Biol 18:220-246.
description: High voltage (1MeV) transmission electron microscopy image of a 0.5 micrometer section through a Chinese hamster ovary cell at metaphase showing a chromatid pair, with kinetochores at the centromere. The image was taken with a specimen tilt of 67 degrees and is one of a group of 10 tilts from 77 degrees to 32 degrees at 5 degree intervals. Pairs of images provide oblique stereo views of the chromosome.
DOI: 10.6075/j08p5z5j
title: CIL:37175, Rattus, kidney cell. In Cell Image Library

description: Relevant citations: 
Kanwar, Y.S. and M.G. Farquhar. 1979. J. Cell Biol. 81:137-153.
Farquhar, M.G., S.L. Wisssig and G.E. Palade. 1961 . J. Exp. Med. 113:47-66.

Original 3.25 in. x 4 in. lantern slides were scanned at 600dpi. Original magnification 8,000X.
description: Transmission electron micrograph of kidney nephrotic glomerulus. The series of images in this group have particular historic and cell biologic importance for determining the role of the glomerular basement membrane in urinary filtration, especially the charge properties and size selectivity in retention of proteins in the circulation. The images here clearly show the glomerular filtration barrier. The study also elucidated the role of the basement membrane in some forms of nephrosis. Image made available by James D. Jamieson and the Department of Cell Biology, Yale University School of Medicine.
description: Preparation: osmium tetroxide fixed tissue
Relation to intact cell: sectioned tissue
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
DOI: 10.5281/zenodo.16919346
title: Systematic Enhancer Mapping and Functional Analysis in Zebrafish with Optimized CRISPR Interference

description: Optimization and Application of CRISPRi for Cis-Regulatory Element Analysis in Zebrafish Embryos

 

ATAC-seq

Publicly available ATAC-seq data for wild-type zebrafish embryos at 48 hpf were obtained from the NCBI Sequence Read Archive (SRA) under the following accessions:





SRA run: SRR12435907 (corresponding to SRX8931602)


SRA run: SRR12435908 (corresponding to SRX8931603)


ATAC-seq data analysis was conducted using the workflow described in the document available at the following link:



ATAC Workflow


 

ChIP-Seq

Publicly available ChIP-Seq (H3k27ac) data for wild-type zebrafish embryos at 48 hpf were obtained from NCBI under the accession number: PRJNA821001 ;

This dataset is also available from the DANIO-CODE database (https://danio-code.zfin.org/dataExport/).

The data processing workflow for ChIP-Seq can be found in this file:

./ChIP-Seq.sh

 

Hi-C

The raw sequencing data generated by our assays has been deposited on China National Center for Bioinformation (CNCB, https://www.cncb.ac.cn/ ), with the project number: PRJCA049852

In this study, we employed the following files as part of the Hi-C data analysis pipeline:

./Hi-C_code.sh

 

Other Datasets

The bw, BED, and BEDPE files used or generated in this study have also been uploaded.

 

Contact



Jiulin Chan ( jlchan@shou.edu.cn )

Peng Hu ( penghu@upenn.edu )

Xiaolong Li ( lixllil@163.com )
DOI: 10.5281/zenodo.17407409
title: Systematic Enhancer Mapping and Functional Analysis in Zebrafish with Optimized CRISPR Interference

description: Optimization and Application of CRISPRi for Cis-Regulatory Element Analysis in Zebrafish Embryos

 

ATAC-seq

Publicly available ATAC-seq data for wild-type zebrafish embryos at 48 hpf were obtained from the NCBI Sequence Read Archive (SRA) under the following accessions:





SRA run: SRR12435907 (corresponding to SRX8931602)


SRA run: SRR12435908 (corresponding to SRX8931603)


ATAC-seq data analysis was conducted using the workflow described in the document available at the following link:



ATAC Workflow


 

ChIP-Seq

Publicly available ChIP-Seq (H3k27ac) data for wild-type zebrafish embryos at 48 hpf were obtained from NCBI under the accession number: PRJNA821001 ;

This dataset is also available from the DANIO-CODE database (https://danio-code.zfin.org/dataExport/).

The data processing workflow for ChIP-Seq can be found in this file:

./ChIP-Seq.sh

 

Hi-C

The raw sequencing data generated by our assays has been deposited on China National Center for Bioinformation (CNCB, https://www.cncb.ac.cn/ ), with the project number: PRJCA049852

In this study, we employed the following files as part of the Hi-C data analysis pipeline:

./Hi-C_code.sh

 

Other Datasets

The bw, BED, and BEDPE files used or generated in this study have also been uploaded.

 

Contact



Jiulin Chan ( jlchan@shou.edu.cn )

Peng Hu ( penghu@upenn.edu )

Xiaolong Li ( lixllil@163.com )
DOI: 10.5281/zenodo.17493237
title: Data_Analysis toward Blind Box Products
DOI: 10.5281/zenodo.17493238
title: Data_Analysis toward Blind Box Products
DOI: 10.6075/j02b8x15
title: CIL:8952, Homo sapiens, epithelial cell. In Cell Image Library

description: Preparation: living tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: spinning disk confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: X-Rhodamine
Processing history: unprocessed raw data
description: Microtubule dynamics in a U2OS (human osteosarcoma) cell. Cells were injected with Xrhodamine-tubulin and this time-lapse image series was collected on a spinning disk confocal microscope on a Nikon Ti200 using a 100X 1.4 NA Plan Apo objective with a 605x52 EM filter for 568 nm laser excitation. Images were collected with a Coolsnap HQ2 (Photometrics) with 700 ms exposure.
DOI: 10.6075/j06h4gg2
title: CIL:8951, Mus musculus, blood vessel endothelial cell, primary cell line cell. In Cell Image Library

description: Individual Mouse Aortic Endothelial Cell (MAEC) migrating in a 3-dimensional collagen gel (1.4mg/mL). Imaged on a spinning disk confocal microscope using a 100x oil immersion objective lens on a Nikon Eclipse Ti equipped with Perfect Focus System, an electronic shutter (Smart shutter, Sutter Instruments; Novato, CA) for transmitted illumination, a linear-encoded X, Y, Z robotic stage with a piezo-driven Z-axis top plate (ASI Technologies, Montgomeryville, PA) and a Yokogawa CSU-X spinning disk confocal scan head in an electronic filterwheel. Total imaging time = 1hr, 12mins.
description: Preparation: living tissue
Relation to intact cell: dispersed cells in vitro; cells in 3D matrix
Item type: recorded image
Imaging mode: phase contrast microscopy; spinning disk confocal microscopy
Parameter imaged: elastic scattering of photons
Source of contrast: differences in amount of elastic light scattering
Visualization methods: visualization of contiguous regions
Processing history: unprocessed raw data
DOI: 10.15468/dl.jnabsr
title: Occurrence Download

description: A dataset containing 5215 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Begonia cucullata"
 ]
}

 The dataset includes 5215 records from 303 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009709-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.60712/si-id371879.1
title: StrainInfo SI-ID 371879.1

description: StrainInfo dataset 371879 about a strain of Lysinibacillus sphaericus. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id371946.1
title: StrainInfo SI-ID 371946.1

description: StrainInfo dataset 371946 about a strain of Bacillus. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id371947.1
title: StrainInfo SI-ID 371947.1

description: StrainInfo dataset 371947 about a strain of Lysinibacillus sphaericus. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id371948.1
title: StrainInfo SI-ID 371948.1

description: StrainInfo dataset 371948 about a strain of Lysinibacillus sphaericus. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id371949.1
title: StrainInfo SI-ID 371949.1

description: StrainInfo dataset 371949 about a strain of Lysinibacillus sphaericus. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id371987.1
title: StrainInfo SI-ID 371987.1

description: StrainInfo dataset 371987 about a strain of Lysinibacillus sphaericus. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.15468/dl.pb3mmg
title: Occurrence Download

description: A dataset containing 26769 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Megapodius Gaimard, 1823"
 ]
}

 The dataset includes 26769 records from 77 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003814-180412121330197/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.60712/si-id371988.1
title: StrainInfo SI-ID 371988.1

description: StrainInfo dataset 371988 about a strain of Lysinibacillus sphaericus. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.5281/zenodo.17327244
title: translate_faroese.csv
DOI: 10.5281/zenodo.17327245
title: translate_faroese.csv
DOI: 10.15468/dl.kb32fa
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Abutilon fruticosum",
 "Country is Qatar",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011660-251009101135966/datasets/export for details.
DOI: 10.15468/dl.y9txhd
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Abutilon fruticosum",
 "Country is Seychelles",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011661-251009101135966/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/inscriptifact-ouc112045634
title: Cuneiform Tablet 1913.14.0169, Spurlock 1913.14.0169

description: [Text Description:] Administrative tablet ❧ [Text or Publication Number Note:] Spurlock 1913.14.0169; CDLI P420550 ❧ [Medium:] Clay ❧ [Script Note:] Non-Alphabetic Cuneiform ❧ [Physical Object Description:] Yellowish White (10YR 9/2) Brownish Pink (5YR 8/3) ❧ [Physical Object Note:] 7.5 x 4.5 x 2.3 cm (82g) ❧ [Physical Object Note:] Seal impressions
DOI: 10.15468/dl.ktp97j
title: Occurrence Download

description: A dataset containing 3377384 species occurrences available in GBIF matching the query:
(Query is too complex. Can be viewed on the landing page)

 The dataset includes 3377384 records from 2004 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0236086-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.agpkq3
title: Occurrence Download

description: A dataset containing 12314 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Country is Honduras",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Liliopsida"
 ]
}

 The dataset includes 12314 records from 62 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0229813-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gzaegr
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Trichocera regelationis Linnaeus, 1758",
 "HasCoordinate is true",
 "Country is Japan",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0192655-220831081235567/datasets/export for details.
DOI: 10.15468/dl.t52ufg
title: Occurrence Download

description: A dataset containing 1454 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Occurrence evidence)",
 "Country is United States of America",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Lutjanus campechanus (Poey, 1860)"
 ]
}

 The dataset includes 1454 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0242367-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.b8jjh8
title: Occurrence Download

description: A dataset containing 165 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (Cameroon, Equatorial Guinea)",
 "OccurrenceStatus is Present",
 "TaxonKey is Adenocarpus mannii (Hook.f.) Hook.f."
 ]
}

 The dataset includes 165 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0244885-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nmhv4v
title: Occurrence Download

description: A dataset containing 424 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "OccurrenceStatus is Present",
 "TaxonKey is Acer miyabei Maxim."
 ]
}

 The dataset includes 424 records from 60 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0192657-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pxvfxy
title: Occurrence Download

description: A dataset containing 126 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Acrocephalus dumetorum Blyth, 1849",
 "HasCoordinate is true",
 "Country is Norway",
 "DatasetKey is Norwegian Species Observation Service",
 "Year is 2013",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 126 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0252910-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.my4v5c
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Thailand",
 "DatasetKey is iNaturalist Research-grade Observations",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Curcuma candida (Wall.) Techapr. & Škorničk.",
 "Year 2000-2024"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0066437-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ah9wac
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Bixa orellana L.",
 "HasCoordinate is true",
 "Country is Japan",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0192669-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nt8qvr
title: Occurrence Download

description: A dataset containing 13382 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Greece",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Boraginales",
 "Year 1000-2022"
 ]
}

 The dataset includes 13382 records from 47 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0242371-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sag5sh
title: Occurrence Download

description: A dataset containing 127 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Sciurus niger avicennia A.H.Howell, 1919",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "DecimalLongitude is -88, -80",
 "DecimalLatitude is 24, 32"
 ]
}

 The dataset includes 127 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0244884-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xz2e53
title: Occurrence Download

description: A dataset containing 16644 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Country is United States of America",
 "OccurrenceStatus is Present",
 "StateProvince is South Dakota",
 "TaxonKey is Mammalia"
 ]
}

 The dataset includes 16644 records from 60 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0254379-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.