cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.17489849
title: Ped-sim def files and simulated segments from 100,000 pairs of 1st through 8th cousins

description: Ped-sim simulates IBD segments (and/or genetic data) for relatives. This repository includes Ped-sim def files for simulating 1st through 8th cousins (3rd through 17th degree relatives), including both full and half-relatives. It also contains simulated IBD segments from 100,000 pairs for each relationship using these def files and summary statistics of the IBD sharing between pairs in the .tot files. Pairs with zero IBD shared are not present in these files. See README.md in ped-sim-defs.zip for bash code used to simulate and to generate the .tot files.

The data were generated using four different crossover models: sex-specific genetic maps + crossover interference (ss_intf), sex-averaged map + crossover interference (sa_intf), sex-specific genetic maps + Poisson crossover localization (ss_poiss), sex-averaged map + Poisson crossover localization (sa_poiss).
DOI: 10.6084/m9.figshare.30497247.v1
title: Additional file 3 of Do duplication-inducing elements ‘cooperate’ with genes in evolutionary arms races? A case study on cereal crop pathogenesis

description: Supplementary Material 3.
DOI: 10.6084/m9.figshare.30497250
title: Additional file 4 of Do duplication-inducing elements ‘cooperate’ with genes in evolutionary arms races? A case study on cereal crop pathogenesis

description: Supplementary Material 4.
DOI: 10.6084/m9.figshare.30497250.v1
title: Additional file 4 of Do duplication-inducing elements ‘cooperate’ with genes in evolutionary arms races? A case study on cereal crop pathogenesis

description: Supplementary Material 4.
DOI: 10.15468/dl.ftccyy
title: Occurrence Download

description: A dataset containing 93 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Colombia",
 "TaxonKey is Hevea brasiliensis",
 "Year 2015-2020"
 ]
}

 The dataset includes 93 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009310-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.33vvt6
title: Occurrence Download

description: A dataset containing 20818 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Acer pictum",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Human Observation)",
 "OccurrenceStatus is Present",
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than or equal to 10000",
 "CoordinateUncertaintyInMeters is null"
 ]
 },
 "EventDate is greater than or equal to 1991-01-01",
 "EventDate is less than or equal to 2025-10-31"
 ]
}

 The dataset includes 20818 records from 140 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009311-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.30497277
title: Additional file 1 of A haplotype-resolved chromatin landscape connects cis-regulatory variants to trait variation in Citrus

description: Supplementary Material 1.
DOI: 10.6084/m9.figshare.30497283
title: Additional file 3 of A haplotype-resolved chromatin landscape connects cis-regulatory variants to trait variation in Citrus

description: Supplementary Material 3.
DOI: 10.6084/m9.figshare.30497295
title: Additional file 2 of Disease-specific epigenetic deregulation of enhancers, transposons, and polycomb targets in acute promyelocytic leukemia

description: Additional file 2: Table S1. Mutations in APL and AML cases and cytogenetics of APL cases. Table S2. Results from MEME motif analysis of APL-specific enhancer regions. Table S3. Gene Ontology enrichment based on motifs identified in APL-specific enhancer regions. Table S4. Correlation between ChromHMM-defined enhancers and gene expression. Table S5. Functional enrichment (KEGG, Reactome, Hallmark) of genes significantly associated with ChromHMM-defined enhancers. Table S6. Genes significantly associated with APL-specific super-enhancers.
DOI: 10.6084/m9.figshare.30497294
title: Additional file 1 of Ex vivo lung-organoid model for aberrant basaloid cell induction and activation

description: Supplementary Material 1. Supplementary Table S1. SingleR score of human ABC_1 and ABC_2 with statistical significance.
DOI: 10.6084/m9.figshare.30497297
title: Additional file 2 of Ex vivo lung-organoid model for aberrant basaloid cell induction and activation

description: Supplementary Material 2. Supplementary Table S2. Differentially expressed genes (DEGs) of AT2 cells between untreated and BLM-stimulated lung organoids.
DOI: 10.6075/j0805230
title: CIL: 51849, Mus musculus, RAW 264.7 TIB-71. In Cell Image Library

description: ~1200 cells were imaged on glass. More gradual additions of drug or carrier were carried out in four equal increments at 0, 30, 60, 90 min, together yielding the same final drug concentration indicated in rapid addition studies. The subpopulation of ~100 cells with extended, leading edge pseudopods at t = 0 were imaged and counted in each unit area at the indicated timepoints during a 125 min observation period T=37C

Images are provided as uncorrected, 16 bit .nd2 files to preserve all original data. To view these .nd2 files:
1. Download ImageJ viewer at (https://imagej.nih.gov/ij/download.html)
2. Download the BioFormats.jar package at (https://www.openmicroscopy.org/bio-formats/downloads/)
3. Open the ImageJ directory after installation and drag the extracted BioFormats.jar package into the "Plugins" subdirectory
4. Open an .nd2 image using imageJ and select opening options when prompted, if desired. If no modifications are desired, select "OK"
5. The 16 bit image will typically look dark and will require brightness adjustment.
6. In the ImageJ toolbar, select Image &gt;&gt; Adjust &gt;&gt; Brightness/Contrast and select "Auto", or manually set the brightness and contrast.
description: A novel cell population analysis to quantify both initial and long-term drug effects, namely pseudopod adaptation and recovery following an initial drug-induced perturbation, adding drug slowly in 1/4 increments over 90 minutes.
description: Imaging mode: DICM
Visualization methods: Spinning disc confocal DICM & widefield DICM Using a Nikon TiE microscope equipped with a 40x, 0.95 N.A. objective and a Hamamatsu ORCA-Flash 4.0 V3 Digital CMOS camera, or a Nikon TiE spinning-disc confocal microscope equipped with a Yokogawa CSU-X1 scanning unit, an Andor iXon 888 EMCCD camera, and a 60x, 1.3 N.A. water-immersion objective or a 40x, 0.95 N.A. objective
DOI: 10.6075/j03t9g70
title: CIL:8050, Mus musculus. In Cell Image Library

description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: quantity of GFP-protein
Visualization methods: Green fluorescent proteins from Anthozoa
Processing history: unprocessed raw data
description: Fluorescence recovery after photobleaching (FRAP)kinetics of MeCP2 were recorded using a mouse fibroblast cell line stably expressing MeCP2-GFP. Live cells were imaged using a Zeiss LSM 510 meta confocal microscope with fluorescence excitation at 488 nm and a 63x plan-apo oil lens. The image series has 2 pre-bleach shots, one immediately after bleaching a 1 micrometer diameter circle of pericentromeric heterochromatin, followed by 103 images at 2 sec intervals.
DOI: 10.6075/j0pk0fj2
title: CIL:45818, Homo sapiens. In Cell Image Library

description: Plate 24775 - Phenotypic profiling attempts to summarize multiparametric, feature-based analysis of cellular phenotypes of each sample so that similarities between profiles reflect similarities between samples. This image set provides a basis for testing image-based profiling methods wrt. to their ability to distinguish the effects of small molecules.
 
Images
The images are of U2OS cells treated with each of 1600 known bioactive compounds and labeled with six labels that characterize seven organelles (the .cell-painting. assay).
 
This pilot experiment consists of 20 plates. Each plate has 384 wells and each well has 9 fields of view for a total of 69,120 fields of view. Each field was imaged in five channels (detection wavelengths), and each channel is stored as a separate, grayscale image file, so there are 345,600 image files in 16-bit TIFF format.
description: Gustafsdottir et al. (doi:10.1371/journal.pone.0080999) have developed a multiplex cytological profiling assay that "paints the cell" with as many fluorescent markers as possible without compromising our ability to extract rich, quantitative profiles in high throughput. The assay detects seven major cellular components. In a pilot screen of bioactive compounds, the assay detected a range of cellular phenotypes and it clustered compounds with similar annotated protein targets or chemical structure based on cytological profiles. The results demonstrate that the assay captures subtle patterns in the combination of morphological labels, thereby detecting the effects of chemical compounds even though their targets are not stained directly. This image-based assay provides an unbiased approach to characterize compound- and disease-associated cell states to support future probe discovery.

Using the cell-painting assay, the Broad Institute has assembled a reference dataset of profiles for U2OS osteosarcoma cells treated with ~30,000 compounds. The compound collection includes DOS-derived compounds (20,000), as well as chemically diverse MLI compounds with biologically diverse performance identified through analysis of PubChem (10,000), and known bioactive compounds to serve as landmarks (2,500). The DOS compounds consist of structurally diverse and stereochemically rich compounds with structures distinct from the current MLSMR. The compound collection also includes 267 distinct compounds nominated by MLPCN Centers from projects for which the Centers would like to identify new chemical series with similar activities.

The experiment consists of 413 microtiter plates. Each plate has 384 wells. Each well has 9 fields of view. Each field was imaged in five channels (detection wavelengths), and each channel is stored as a separate, grayscale 16-bit TIFF image file.
DOI: 10.6075/j0xg9q33
title: CIL:36526, Xenopus laevis, fertilized egg. In Cell Image Library

description: Images collected on a Zeiss LSM 710 confocal with a 10X 0.3 NA objective using 561 and 633 laser lines.
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).
DOI: 10.6075/j0j67fz2
title: CIL:2687, Caenorhabditis elegans. In Cell Image Library

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: 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: 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 8 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/j0k93770
title: CIL: 54119, Homo sapiens, HeLa. In Cell Image Library

description: Visualization methods: confocal microscopy
description: TK 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: 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.
DOI: 10.6075/j0w37vxn
title: CIL: 52975, Homo sapiens, High-grade serious overian cancer. In Cell Image Library

description: One z layer of a z-stack at the given image
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: Image 5, z=5 from SC_011
DOI: 10.6075/j0nk3crr
title: CIL:13382, Homo sapiens, mammary epithelia (MEC). In Cell Image Library

description: Preparation: formaldehyde fixed tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: differences in adsorption or binding of stain
Visualization methods: Alexa Fluor 488; 4',6-diamidino-2-phenylindole (DAPI)
Processing history: unprocessed raw data
description: The nucleolus during mammary epithelial differentiation and early mammary tumorigenesis. Proliferating 3D cultures of MCF-10.B2 cells at day 20 were stained with ANA-N antibody to detect nucleoli (green) and counterstained with DAPI to delineate nuclei (blue). Under these conditions, cells form acini. The stack shown is presented as a projected image in Fig 1A (Day 20 control)of Meaburn and Misteli, 2008 J Cell Biol 180:39-50.
The z-series was recorded with a Zeiss LSM 510 META confocal microscope with a 63x 1.4 NA objective lens.
DOI: 10.6075/j0sb44nq
title: CIL:41019, Haematococcus pluvialis. In Cell Image Library

description: Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: phase contrast microscopy
Parameter imaged: elastic scattering of photons
Source of contrast: differences in amount of elastic light scattering
Visualization methods: visualization of contiguous regions
description: Phase contrast image of fresh water unicellular algae Haematococcus pluvialis colelcted at 100X. This species is well known for its high content of the strong antioxidant astaxanthin, which is important in aquaculture, various pharmaceuticals, and cosmetics. Fourth Prize, 2009 Olympus BioScapes Digital Imaging Competition©
DOI: 10.6075/j0028r5h
title: CIL: 53405, Plankton. In Cell Image Library

description: Imaging mode: Holography
Visualization methods: Amplitude Mode
description: 128x128 segmented image from volumetric hologram
description: Ciliate
DOI: 10.6075/j0nk3ctn
title: CIL:24817, Saccharomyces cerevisiae S288c. In Cell Image Library

description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: EGFP
Processing history: constrained iterative deconvolution
Data qualification: Processed;spatialmeasurements;intensitiesquantitation
description: Intracellular localization of GFP-Vps74 W88A, R97A mutant in BY4742 sac1∆ vps74∆ mutant. SAC1 encodes an integral membrane phosphoinositide phosphatase and in the sac1∆ vps74∆ mutant, GFP-Vps74 localizes, in addition to the Golgi apparatus, to nuclear ER and cortical ER and/or PM (CIL# 24816). This localization of GFP-Vps74 is lost when two amino acids are mutated in the sulfate-binding pocket. This study demonstrates that the sulfate-binding pocket of Vps74 and GOLPH3 mediates PtdIns4P-binding and is essential for function. Cells grown in liquid medium were mounted in growth medium and 3D image stacks were collected at 0.4-µm z increments on a DeltaVision workstation (Applied Precision) based on an inverted microscope (IX-70; Olympus) using a 100× NA 1.4 oil immersion lens. Images were captured at 23C with a 12-bit CCD camera (CoolSnap HQ; Photometrics) and deconvolved using the iterative-constrained algorithm (Agard, 1984) and the measured point spread function. One image from the approximate center of z stack is shown in Fig4A W88A R97A/sac1∆ panel in J Cell Biol. 187: 967-975. 2009. Images in Fig 4A include CIL#s 13449, 13451, 13453, 13455, 13456, 13457, 24816, 24817, 24818, 24819, 24820, 24821.
DOI: 10.6075/j047493p
title: CIL:1134, Caenorhabditis elegans, muscle cell. In Cell Image Library

description: C. elegans muscle age is a data set of fluorescence 20X microscopy images of C. elegans nematodes stained with phalloidin to visualize actin in muscles at different ages (1,2,4, and 8). Note that the data sets for each age can be found by searching for a featured image from each set: CIL 1005, 1057, 1105, and 1265, respectively.
description: The purpose of the dataset C. elegans muscle aging is to deduce the age of the nemathode based on images of muscles. Images of C. elegans were taken at different chronological ages. This image is part of the day 4 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.
description: Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope
Visualization methods: phalloidin
Processing history: unprocessed raw data
DOI: 10.6075/j0fq9w37
title: CIL: 52019, 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: 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
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.
DOI: 10.6075/j06w990d
title: CIL:35661, Saccharomyces cerevisiae. In Cell Image Library

description: The images were acquired using a 60x 1.42 NA objective lens on Delta Vision system equipped with CoolSNAP_HQ2 / HQ2-ICX285. Please see the microscopy section in the referenced manuscript for details for image analysis.
description: A time lapse experiment of Saccharomyces cerevisiae expressing GFP tagged Cdc6. Cdc 6 is an essential ATP-binding protein required for DNA replication, component of the pre-replicative complex (pre-RC) which requires ORC to associate with chromatin and is in turn required for Mcm2-7p DNA association; homologous to S. pombe Cdc18p.These phase,gfp images are part of an image group that ranges from CIL:35660-35679. Note that there are additional groups showing time series of other cell cycle regulation proteins by the same authors in the Library.
description: Preparation: living tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: fluorescence microscopy; phase contrast microscopy
Parameter imaged: fluorescence emission; elastic scattering of photons
Source of contrast: distribution of a specific protein; differences in amount of elastic light scattering
Visualization methods: EGFP; visualization of contiguous regions
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements
DOI: 10.6075/j0tq60t5
title: CIL:1148, Caenorhabditis elegans, muscle cell. In Cell Image Library

description: C. elegans muscle age is a data set of fluorescence 20X microscopy images of C. elegans nematodes stained with phalloidin to visualize actin in muscles at different ages (1,2,4, and 8). Note that the data sets for each age can be found by searching for a featured image from each set: CIL 1005, 1057, 1105, and 1265, respectively.
description: The purpose of the dataset C. elegans muscle aging is to deduce the age of the nemathode based on images of muscles. Images of C. elegans were taken at different chronological ages. This image is part of the day 4 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.
description: Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope
Visualization methods: phalloidin
Processing history: unprocessed raw data