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544 results for “HeLa cells”
STING OPS: HeLa Genome-wide Screen Single-Cell Features (Part 4/5)
<div> <div> <p><strong>Classification and functional characterization of regulators of intracellular STING trafficking identified by genome-wide optical pooled screening</strong></p> <p>Single-cell features and coordinates for HeLa genome-wide screen, Zenodo dataset part 4/5.</p> <p>Images available at gs://opspublic-east1/STINGOpticalPooledScreen/Images/GW*.</p> <p>README for additional image information is at gs://opspublic-east1/STINGOpticalPooledScreen/STING_README.</p> </div> </div>
Targeted Illumination in HeLa Cells
<p>Files are a time series of showing targeted illumination of a subset of HeLa cell nuclei containing a photolabile ATAC-seq library. Time points are 300 ms apart. The single-channel images were acquired using a spinning disk confocal with a 40X objective (Nikon MRD77410) using a 561 nm laser line and 525/36 emission filter (MVI, 77074803). Images were captured using a Zyla 2.3 PLUS sCMOS camera. The pixel value represents the fluorescence intensity of the photocleavable fluorophore attached to the fragment library. Images are acquired concurrently with targeted illumination using a 405 nm laser line.</p>
PARK15/FBXO7 is dispensable for PINK1/Parkin mitophagy in iNeurons and HeLa cell systems
<p>The protein kinase PINK1 and ubiquitin ligase Parkin promote removal of damaged mitochondria via a feed-forward mechanism involving ubiquitin (Ub) phosphorylation, Parkin activation, and ubiquitylation of mitochondrial outer membrane proteins to support recruitment of mitophagy receptors. The ubiquitin ligase substrate receptor FBXO7/PARK15 is mutated in an early-onset parkinsonian-pyramidal syndrome. Previous studies have proposed a role for FBXO7 in promoting Parkin-dependent mitophagy. Here, we systematically examine the involvement of FBXO7 in depolarization-dependent mitophagy in the well-established HeLa and induced-neurons cell systems. We find that FBXO7<sup>-/-</sup> cells have no demonstrable defect in: 1) kinetics of pUb accumulation, 2) pUb puncta on mitochondria by super-resolution imaging, 3) recruitment of Parkin and autophagy machinery to damaged mitochondria, 4) mitophagic flux, and 5) mitochondrial clearance as quantified by global proteomics. Moreover, global proteomics of neurogenesis in the absence of FBXO7 reveals no obvious alterations in mitochondria or other organelles. These results argue against a general role for FBXO7 in Parkin-dependent mitophagy and point to the need for additional studies to define how FBXO7 mutations promote parkinsonian-pyramidal syndrome. </p>
AFM Dataset on HeLa cells
<p>Dataset acquired using a NanoWizard III (Bruker, Santa Barbara, CA, USA) on 40 HeLa cells using a SAA-SPH-5UM AFM probe (Bruker, Santa Barbara, CA, USA).</p> <p>The dataset includes force maps (20 cells) and microrheological measurements (20 cells) acquired on HeLa cells.</p> <p>Additionally this dataset includes:</p> <p>- Force settings used to acquired the data</p> <p>- Data used to characterize the piezo lag</p> <p>- Data used to characterize the viscous drag</p> <p>- Results obtained from PyFMLab, MATLAB routines and JPKDP</p>
2D phase contrast HeLa cells images with ground truth annotations
<p>Original images are from http://www.robots.ox.ac.uk/~vgg/software/cell_detection/. This software is associated with the publication "Learning to Detect Cells Using Non-overlapping Extremal Regions", MICCAI 2012. (DOI: 10.1007/978-3-642-33415-3_43)</p> <p>Here, we provide the ground truth labels of: cell centers and segmentation, which are used in the publications:</p> <ul> <li>"Learning to Segment: Training Hierarchical Segmentation under a Topological Loss", MICCAI 2015. (DOI: 10.1007/978-3-319-24574-4_32)</li> <li>"Cell Detection and Segmentation Using Correlation Clustering", MICCAI 2014. (DOI: 10.1007/978-3-319-10404-1_2)</li> </ul>
Polarisation camera dSTORM datasets of actin in fixed HeLa cells labeled with phalloidin-Alexa Fluor 488
<p>Polarisation camera dSTORM dataset of the actin of fixed HeLa cells labeled with phalloidin-Alexa Fluor 488.</p> <p><strong>Image acquisition was performed as follows:</strong></p> <p>Imaging was performed on a widefield microscope equipped with a polarisation camera (CS505MUP, Thorlabs). The sample was excited using a 488 nm laser at quasi-TIRF, with a measured power density at the image plane of <span>5.04 kW/cm^2</span>. A single long-pass dichroic (Di02-R488, Semrock) was used to seperate fluorescence from the excitation. The emission was filtered using a long-pass (BLP01-488R, Semrock) and a bandpass filter (FF01-582/64, Semrock) before detection. An exposure time of 30 ms was used.</p> <p><strong>Samples were prepared as follows:</strong></p> <p><span>Cell culture: </span>HeLa TDS cells were cultured in DMEM (Gibco, Invitrogen) supplemented with 10 % Fetal Bovine Serum (FBS, Life Technologies), 1 % penicillin/streptomycin (Life Technologies), and 1 % glutamine (Life Technologies) at 37 °C + 5 % CO_2. Cells were periodically tested for mycoplasma contamination and passaged 3 times per week. Cells were plated at low density on high-precision glass coverslips (MatTek, P35G-0.170-14-C) 1 day prior to fixation for dSTORM experiments.</p> <p><span>Labeling:</span> Cells were simultaneously fixed and permeabilized in cytoskeleton buffer (CBS, 10 mM MES, 138 mM KCl, 3 mM MgCl_2, 2 mM EGTA, 4.5 % sucrose w/v, pH 7.4), + 4 % paraformaldehyde (PFA) and 0.2 % Triton for 6 minutes at 37 °C, and further fixed in CBS + 4 % PFA for 14 minutes at 37 °C. Post-fixation, cells were washed x3 in PBST (PBS supplemented with 0.1 % Tween) and permeabilized a second time in PBS + 0.5 % Triton for 5 minutes at room temperature. The samples were then washed 3 times in PBST and blocked for 30 minutes in 5 % BSA. Cells were washed x3 in PBST and then incubated with Alexa Fluor™ 488 Phalloidin (A12379, Invitrogen, 1:50 in PBS) for 1 h in the dark, followed by x2 washes in PBS. Prior to dSTORM imaging, PBS was replaced with dSTORM imaging buffer (base buffer consisting of 0.56 M glucose, 50 mM Tris (pH 8.5), and 10 mM NaCl supplemented with 5 U/mL pyranose oxidase (Sigma, P4234), 10 mM cysteamine (Sigma, 30070), 40 µg/mL catalase (Sigma, C100) and 2 mM cyclooctatetraene (Sigma, 138924).</p>
Polarisation camera dSTORM datasets of actin in fixed HeLa cells labeled with phalloidin-Alexa Fluor 647
<p>Polarisation camera dSTORM dataset of the actin of fixed HeLa cells labeled with phalloidin-Alexa Fluor 647.</p> <p><strong>Image acquisition was performed as follows:</strong></p> <p>Imaging was performed on a widefield microscope equipped with a polarisation camera (CS505MUP, Thorlabs). The sample was excited using a 638 nm laser at quasi-TIRF, with a measured power density at the image plane of 3.51 kW/cm^2. A multiband dichroic (Di03-R405/488/561/635-t1, Semrock) was used to seperate fluorescence from the excitation. The emission was filtered using a long-pass filter (BLP01-635R, Semrock) before detection. An exposure time of 30 ms was used.</p> <p><strong>Samples were prepared as follows:</strong></p> <p>Cell culture: HeLa TDS cells were cultured in DMEM (Gibco, Invitrogen) supplemented with 10 % Fetal Bovine Serum (FBS, Life Technologies), 1 % penicillin/streptomycin (Life Technologies), and 1 % glutamine (Life Technologies) at 37 °C + 5 % CO_2. Cells were periodically tested for mycoplasma contamination and passaged 3 times per week. Cells were plated at low density on high-precision glass coverslips (MatTek, P35G-0.170-14-C) 1 day prior to fixation for dSTORM experiments.</p> <p>Labeling: Cells were simultaneously fixed and permeabilized in cytoskeleton buffer (CBS, 10 mM MES, 138 mM KCl, 3 mM MgCl_2, 2 mM EGTA, 4.5 % sucrose w/v, pH 7.4), + 4 % paraformaldehyde (PFA) and 0.2 % Triton for 6 minutes at 37 °C, and further fixed in CBS + 4 % PFA for 14 minutes at 37 °C. Post-fixation, cells were washed x3 in PBST (PBS supplemented with 0.1 % Tween) and permeabilized a second time in PBS + 0.5 % Triton for 5 minutes at room temperature. The samples were then washed 3 times in PBST and blocked for 30 minutes in 5 % BSA. Cells were washed x3 in PBST and then incubated with Alexa Fluor™ 647 Phalloidin (A22287, Invitrogen, 1:50 in PBS) for 1 h in the dark, followed by x2 washes in PBS. Prior to dSTORM imaging, PBS was replaced with dSTORM imaging buffer (base buffer consisting of 0.56 M glucose, 50 mM Tris (pH 8.5), and 10 mM NaCl supplemented with 5 U/mL pyranose oxidase (Sigma, P4234), 10 mM cysteamine (Sigma, 30070), 40 µg/mL catalase (Sigma, C100) and 2 mM cyclooctatetraene (Sigma, 138924).</p>
Hela Cell dataset with annotations for dividing and non dividing cells (TYX)
<p>This dataset was created to be used for training ONEAT networks. Each movie is accompanied by 2 csv files, one containing the location of dividing cells and other one containing the location of non-dividing cells. The training data was created using yoloneat-viz repo: https://github.com/Kapoorlabs-paris/yoloneat-viz/blob/main/examples/TrainingDataMaker.ipynb. The notebook can be modified to include N types of cell events and the program is in no way limited to creating classification of just 2 type of cell events. </p>
Training dataset of Hela cells for oneat network training
<p>Here we present the tif files to be used to trainthe Oneat networks for detection of division events for Hela cells imaged under different imaging modalities and presented originally here: https://zenodo.org/record/6139958#.Yjcjl3rMJD8</p>
Single-Cell Imaging Dataset: Hela FUCCI Cell Fluorescence Analysis
<p>Hela FUCCI Cell Dataset: Fluorescence Intensity and Segmentation</p> <p>The "Hela FUCCI Cell Dataset" is a comprehensive collection of fluorescence microscopy data capturing the fluorescence intensity of Hela FUCCI cells. The dataset encompasses a diverse range of cellular images acquired through fluorescence imaging techniques, offering valuable insights into the cellular behavior and fluorescent signal patterns.</p> <p>Contents:</p> <p>Fluorescence Intensity Data: The dataset includes fluorescence images of Hela FUCCI cells captured in both red and green channels. These images represent the intensity levels of cellular fluorescence signals.</p> <p>Purpose:<br> The dataset serves as a resource for researchers and scientists interested in cellular fluorescence analysis. It supports investigations into cellular dynamics, cell cycle studies, and fluorescence signal patterns. Researchers can utilize this dataset to develop and evaluate image processing, analysis, and machine learning techniques for cell detection and fluorescence quantification.</p> <p>Data Collection:<br> The data were collected using fluorescence microscopy techniques, capturing the distinct fluorescence signals emitted by Hela FUCCI cells. </p> <p>Usage:<br> Researchers can use this dataset to:</p> <p>Investigate fluorescence patterns and intensities of Hela FUCCI cells.<br> Develop and validate machine learning algorithms for cell segmentation and detection.<br> Explore cellular behaviors and dynamics under various experimental conditions.</p> <p>Citation:<br> If you use this dataset in your research, please cite the original source to acknowledge its contribution.</p> <p>Access and Availability:<br> The dataset is openly available through Zendo, accessible via the following link: https://zenodo.org/. Researchers are encouraged to explore, analyze, and contribute to the dataset's applications and advancements in cellular fluorescence analysis.</p>
High throughput measurement of single HeLa cell volume growth and cell cycle progression using FXm
Open the record for dataset details and reuse information.
Epigenomic profiling of TASOR in Hela cells using ChIP, CUT&RUN and CUT&Tag
<p>Example bigwig coverage tracks illustrating TASOR-regulated H3K9me3 and TASOR genome binding.</p> <p>Mapped to hg38.</p> <p>For detailed methods, see linked preprint.</p>
LBPA/Cholesterol screen data raw images HeLa MZ cells
<p>Raw images of Prestwick compound screen on HeLa MZ cells</p>
Nascent-seq of HeLa cells after rapid depletion of SRSF5 using hGRAD for 2h, 8h and 16h
GEO Series GSE229324. Homo sapiens. 8 samples. Type: Expression profiling by high throughput sequencing.
Nuclear Scaffold Attachment Sites in HeLa Cells Across 1% of the Human Genome
GEO Series GSE26477. Homo sapiens. 1 samples. Type: Genome binding/occupancy profiling by genome tiling array.
PARCLIP analysis of NONO and SFPQ from U2OS and Hela cells
GEO Series GSE113349. Homo sapiens. 4 samples. Type: Other.
RNA sequencing analysis for cellular metabolic pathway in MARCHF6 Knock-Out HeLa cell lines
GEO Series GSE173282. Homo sapiens. 6 samples. Type: Expression profiling by high throughput sequencing.
Viral determinants in H5N1 influenza A virus enable productive infection of HeLa cells
GEO Series GSE140759. Homo sapiens. 8 samples. Type: Expression profiling by high throughput sequencing.
RNA-seq analysis of HeLa cells in nutrient-rich and nutrient-deprived media
GEO Series GSE211066. Homo sapiens. 12 samples. Type: Expression profiling by high throughput sequencing.
Non-synchronized cell cycle transcriptomics in U2OS and HeLa cancer cells
GEO Series GSE104736. Homo sapiens. 15 samples. Type: Expression profiling by high throughput sequencing.
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.