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34 results for “53BP1”
Nanomaterial genotoxicity evaluation using the high-throughput p53-binding protein 1 (53BP1) assay - data from the article published in PlosOne
<p>Data that have been used in the manuscript "Nanomaterial genotoxicity evaluation using the high-throughput p53-binding protein 1 (53BP1) assay" by M. Fontaine et al., published in PlosOne in 2023.</p>
Confocal microscopy of gH2AX and 53BP1 DNA repair foci of cells exposed to gamma-irradiation, pt. 2/3
<p><strong>Summary</strong></p> <p>Dataset of confocal microscopy data of cells exposed to gamma-irradiation and immunostained with gH2AX and 53BP1.</p> <ul> <li><strong>Part 1/3: </strong>Head and neck primocultures immunostained with gH2AX/53BP1, Testing dataset. DOI <a href="https://doi.org/10.5281/zenodo.2564980">10.5281/zenodo.2564980</a></li> <li><strong>Part 2/3 (this dataset)</strong>: U-87 and NHDF Cells exposed to 1-4 Gy confocal microscopy data of head and neck tumor primocultures immunostained with gH2AX/53BP1. Testing dataset. DOI <a href="https://doi.org/10.5281/zenodo.2572450">10.5281/zenodo.2572450</a>. 174 TIFFs</li> <li><strong>Part 3/3</strong>: training dataset for nuclei and gH2AX foci with ground truth annotation masks, head and neck primocultures (head and neck non-tumor and spinocellular tumor cells). DOI <a href="https://doi.org/10.5281/zenodo.2576241">10.5281/zenodo.2576241</a>. 150 TIFFs for nuclei learning incl 150 png nuclei masks + 99 TIFFs for DNA repair foci training</li> <li><strong>Code</strong>: the code is available at <a href="https://github.com/tomasvicar/LearnFoci">https://github.com/tomasvicar/LearnFoci</a></li> </ul> <p><strong>Materials and methods</strong></p> <p><em>Dataset</em></p> <p>Following cells were used: (1) patient primocultures of patients with spinocellular head and neck tumors (histologically verified tumor and tumor-adjacent tissues), isolation protocol descibed in <em>Svobodova et al, 2017</em>, (2) primary glioblastoma cell line U-87 (ATCC HTB-14, LGC Standards, United Kingdom), (3) primary normal human dermal fibroblasts (NHDF, PromoCell, Hedelberg, Germany) isolated from the dermis of juvenile foreskin or adult skin.<br> The study was conducted in accord with the Helsinki Declaration of 1964 and all subsequent revisions thereof. It was approved by the ethical committee of St. Anne’s Faculty Hospital, Brno. Primoculture cells were cultivated in Pen/Strep antibiotic solution (PAA Laboratories GmbH, Austria) in RPMI-1640 medium with 10% FBS (Biochrom, USA) at 37 °C and 50% CO2 in humidified atmosphere up to 50% confluence. U-87 were grown in Eagle's MEM with 10% FBS.</p> <p><em>Gamma irradiation</em></p> <p>The cells were irradiated at the Institute of Biophysics, Czech Academy of Sciences, Brno, Czech Republic in a following schemes: (a) patient-derived primoculture was irradiated with a single dose of 2 Gy (D = 1 Gy/min) of gamma-rays (60Co, Chisostat, Chirana, CR) , (b) U-87 and NHDF cells were irradiated with doses 1, 2, and 4 Gy (D = 1 Gy/min). Cells were irradiated in RPMI 1640 medium (37 °C, normal atmosphere). Confocal microscopy of gammaH2AX and 53BP1 foci immunodetection was consequently performed.</p> <p><em>Fluorescent staining </em></p> <p>DNA double strand breaks (DSBs) were quantified in different periods of time post-irradiation (30 min, 8h and 24h post irradiation) by means of $\gamma$H2AX and 53BP1 foci immunodetection combined with confocal microscopy. For details see \cite{falk2007chromatin}.</p> <p><em>Confocal microscopy</em></p> <p>The microscopy of samples was performed at the Institute of Biophysics, Czech Academy of Sciences, Brno, Czech Republic. Leica DM RXA microscope (equipped with DMSTC motorized stage, Piezzo z-movement, MicroMax CCD camera, CSU-10 confocal unit and 488, 562, and 714 nm laser diodes with AOTF) was used for acquiring detailed cell images (100× oil immersion Plan Fluotar lens, NA 1.3). Total 50 Z slices was captured with Z step size 0.3 μm.</p> <p><strong>File description</strong></p> <p>all files are compressed hyperstack tiffs (50 Z slices and 3 fluorescent channels, XYCZ order), 100x magnification</p> <ul> <li>Confocal_NHDF_cells_IR_1-4Gy.zip: Human fibroblast NHDF cell line, exposed to gamma irradiation doses 1, 2, and 4 Gy, 64 TIFFs</li> <li>Confocal_U-87_cells_IR_1-4Gy.zip: Human glioblastoma U-87 cell line, exposed to gamma irradiation doses 1, 2, and 4 Gy, 108 TIFFs</li> </ul>
Confocal microscopy of gH2AX and 53BP1 DNA repair foci of cells exposed to gamma-irradiation, pt. 1/3
<p><strong>Summary</strong></p> <p>Dataset of confocal microscopy data of cells exposed to gamma-irradiation and immunostained with gH2AX and 53BP1.</p> <ul> <li><strong>Part 1/3 (this dataset): </strong>Head and neck primocultures immunostained with gH2AX/53BP1, Testing dataset. DOI <a href="https://doi.org/10.5281/zenodo.2564980">10.5281/zenodo.2564980</a></li> <li><strong>Part 2/3</strong>: U-87 and NHDF Cells exposed to 1-4 Gy confocal microscopy data of head and neck tumor primocultures immunostained with gH2AX/53BP1. Testing dataset. DOI <a href="https://doi.org/10.5281/zenodo.2572450">10.5281/zenodo.2572450</a>. 174 TIFFs</li> <li><strong>Part 3/3</strong>: training dataset for nuclei and gH2AX foci with ground truth annotation masks, head and neck primocultures (head and neck non-tumor and spinocellular tumor cells). DOI <a href="https://doi.org/10.5281/zenodo.2576241">10.5281/zenodo.2576241</a>. 150 TIFFs for nuclei learning incl 150 png nuclei masks + 99 TIFFs for DNA repair foci training</li> <li><strong>Code</strong>: the code is available at <a href="https://github.com/tomasvicar/LearnFoci">https://github.com/tomasvicar/LearnFoci</a></li> </ul> <p><strong>Materials and methods</strong></p> <p><em>Dataset</em></p> <p>Following cells were used: (1) patient primocultures of patients with spinocellular head and neck tumors (histologically verified tumor and tumor-adjacent tissues), isolation protocol descibed in <em>Svobodova et al, 2017</em>, (2) primary glioblastoma cell line U-87 (ATCC HTB-14, LGC Standards, United Kingdom), (3) primary normal human dermal fibroblasts (NHDF, PromoCell, Hedelberg, Germany) isolated from the dermis of juvenile foreskin or adult skin.<br> The study was conducted in accord with the Helsinki Declaration of 1964 and all subsequent revisions thereof. It was approved by the ethical committee of St. Anne’s Faculty Hospital, Brno. Primoculture cells were cultivated in Pen/Strep antibiotic solution (PAA Laboratories GmbH, Austria) in RPMI-1640 medium with 10% FBS (Biochrom, USA) at 37 °C and 50% CO2 in humidified atmosphere up to 50% confluence. U-87 were grown in Eagle's MEM with 10% FBS.</p> <p><em>Gamma irradiation</em></p> <p>The cells were irradiated at the Institute of Biophysics, Czech Academy of Sciences, Brno, Czech Republic in a following schemes: (a) patient-derived primoculture was irradiated with a single dose of 2 Gy (D = 1 Gy/min) of gamma-rays (60Co, Chisostat, Chirana, CR) , (b) U-87 and NHDF cells were irradiated with doses 1, 2, and 4 Gy (D = 1 Gy/min). Cells were irradiated in RPMI 1640 medium (37 °C, normal atmosphere). Confocal microscopy of gammaH2AX and 53BP1 foci immunodetection was consequently performed.</p> <p><em>Fluorescent staining </em></p> <p>DNA double strand breaks (DSBs) were quantified in different periods of time post-irradiation (30 min, 8h and 24h post irradiation) by means of $\gamma$H2AX and 53BP1 foci immunodetection combined with confocal microscopy. For details see \cite{falk2007chromatin}.</p> <p><em>Confocal microscopy</em></p> <p>The microscopy of samples was performed at the Institute of Biophysics, Czech Academy of Sciences, Brno, Czech Republic. Leica DM RXA microscope (equipped with DMSTC motorized stage, Piezzo z-movement, MicroMax CCD camera, CSU-10 confocal unit and 488, 562, and 714 nm laser diodes with AOTF) was used for acquiring detailed cell images (100× oil immersion Plan Fluotar lens, NA 1.3). Total 50 Z slices was captured with Z step size 0.3 μm.</p> <p><strong>File description</strong></p> <p>all files are compressed hyperstack tiffs (50 Z slices and 3 fluorescent channels, XYCZ order), 100x magnification</p> <ul> <li>Confocal_HN_tumor_primocultures.zip: dataset of patient-derived primocultures (gamma-irradiated with 2 Gy and controls), for description see file below, 100 FOVs,</li> <li>Confocal_HN_tumor_primocultures_description.xlsx: description of confocal dataset files and patient tumor characteristics</li> <li>Confocal_HN_tumor_primocultures_train_nuclei.zip: annotated training subset 1 of dataset of patient-derived primocultures (gamma-irradiated with 2 Gy and controls) used for nuclei segmentation training, 150 FOVs, includes TIFF and manually annotated binary mask for nuclei (data_###.tif and respective mask_###.png)</li> <li>Confocal_HN_tumor_primocultures_train_nuclei_description.xlsx: description of above-mentioned files (tissue type, TNM stage, grade, time post irradiation)</li> </ul>
Annotated DNA Double Strand Break Ionizing Radiation-Induced Foci (gH2AX 53BP1) Confocal Microscopy, pt. 2
<p><strong>Summary</strong></p> <p>Dataset of confocal microscopy data of cells exposed to gamma-irradiation and immunostained with gH2AX and 53BP1.</p> <ul> <li>Nuclei segmentation Head and neck primocultures immunostained with gH2AX/53BP1, Training/Testing/Validation dataset (nucleus_segmentation.zip) (available in part 1, <a href="https://dx.doi.org/10.5281/zenodo.4067741">https://dx.doi.org/10.5281/zenodo.4067741</a>) </li> <li>IRIF Foci: Head and neck primocultures immunostained with gH2AX/53BP1, Training/Testing/Validation dataset. (foci_detection.zip) (available in part 1, <a href="https://dx.doi.org/10.5281/zenodo.4067741">https://dx.doi.org/10.5281/zenodo.4067741</a>)</li> <li>Cell lines: U-87 and NHDF Cells exposed to 0.5-8 Gy 30 min and 8h post irradiation - confocal microscopy data of gH2AX/53BP1/DAPI annotated for gH2AX, 53BP1 and colocalized foci separately (cell_lines_U87.zip and cell_lines_NHDF.zip, this part of dataset) </li> <li><strong>Code</strong>: the code is available at <a href="https://github.com/tomasvicar/DeepFoci">https://github.com/tomasvicar/DeepFoci</a></li> <li><strong>Preprint: </strong>Vicar et al, DeepFoci: Deep Learning-Based Algorithm for Fast Automatic Analysis of DNA Double Strand Break Ionizing Radiation-Induced Foci, <a href="https://doi.org/10.1101/2020.10.07.321927">10.1101/2020.10.07.321927</a></li> <li><strong>Publication: </strong>Vicar et al, TBA</li> </ul> <p><strong>Materials and methods</strong></p> <p><em>Dataset</em></p> <p>Following cells were used:</p> <p>1) The training/validation/testing datasets was based on patient-derived primary cell cultures prepared from spinocellular tumors and morphologically normal tissues adjacent to the tumor taken from patients suffering from head and neck cancer. The dataset was divided into two subsets: one for training, validation and testing the nucleus segmentation (237/10/30 fields of view (FOVs), respectively) and one for training, validation and testing the focus segmentation (239/60/100 FOVs). The dataset consisted of several cell types: a) tumor cells, b) tumor-associated fibroblasts, and c) cells from morphologically normal tissues. All cell types were fixed at different periods of time (0 (non-irradiated control), 0.5, 8 or 24 h PI) after exposure to 2 Gy of gamma-rays. The representation of cells in two subsets with respect to the cell type and post-irradiation time (i.e., DSB repair duration) was random.</p> <p>2) The evaluation dataset was used to assess the robustness of segmentation procedures. It was composed of multiple types of differently treated cells in order to represent a highly challenging dataset maximally reflecting high biological and technical variability between samples, as it may appear in research or clinical practice. The dataset contained a) mesenchymal NHDF fibroblasts coming from a standard permanent cell line, b) radioresistant U-87 glioblastoma cells coming from a standard permanent cell line, c) tumor cells (CD90-) and tumor-associated fibroblasts (CD90+) prepared as a primary culture from a spinocellular tumors of patients (different from dataset 1) suffering from a head and neck cancer, and d) cells prepared as primary cultures from morphologically normal tissue adjacent to tumors of involved head and neck cancer patients. NHDF and U-87 cells received 0.5, 0, 1, 2, 4 and 8 Gy of gamma-rays and were fixed at 30 min and 8 h post-irradiation, while the primary cultures were only exposed to the dose of 2 Gy (for a limited amount of the cell material) and fixed at 0 (non-irradiated control), 0.5, 8 or 24 h post-irradiation times.</p> <p><em>Gamma irradiation</em></p> <p>The cells were irradiated at the Institute of Biophysics, Czech Academy of Sciences, Brno, Czech Republic in a following schemes: (a) patient-derived primoculture was irradiated with a single dose of 2 Gy (D = 1 Gy/min) of gamma-rays (60Co, Chisostat, Chirana, CR) , (b) U-87 and NHDF cells were irradiated with doses 0.5-8 Gy (D = 1 Gy/min). Cells were irradiated in RPMI 1640 medium (37 °C, normal atmosphere). Confocal microscopy of gammaH2AX and 53BP1 foci immunodetection was consequently performed.</p> <p><em>Fluorescent staining</em></p> <p>DNA double strand breaks (DSBs) were quantified in different periods of time post-irradiation (30 min, 8h and 24h post irradiation) by means of $\gamma$H2AX and 53BP1 foci immunodetection combined with confocal microscopy. For details see \cite{falk2007chromatin}.</p> <p><em>Confocal microscopy</em></p> <p>The microscopy of samples was performed at the Institute of Biophysics, Czech Academy of Sciences, Brno, Czech Republic. Leica DM RXA microscope (equipped with DMSTC motorized stage, Piezzo z-movement, MicroMax CCD camera, CSU-10 confocal unit and 488, 562, and 714 nm laser diodes with AOTF) was used for acquiring detailed cell images (100× oil immersion Plan Fluotar lens, NA 1.3). Total 50 Z slices was captured with Z step size 0.3 μm.</p> <p><strong>File description</strong></p> <p>all files are compressed hyperstack tiffs (50 Z slices and 3 fluorescent channels, XYCZ order), 100x magnification</p> <ul> <li>foci_detection.zip: IRIF Foci (available in part 1, <a href="https://dx.doi.org/10.5281/zenodo.4067741">https://dx.doi.org/10.5281/zenodo.4067741</a>): Head and neck primocultures immunostained with gH2AX/53BP1, Training/Testing/Validation dataset: FOVs 240/100/120 files for training, testing, and validation, organisation: <ul> <li>data_001.tif – 3channel Z.stack tiff</li> <li>mask_001.tif – respective Z stack mask with single points per IRIF focus (manual annotation, training and testing subsets only)</li> <li>data_description.xlsx – description of sample type (2Gy post irradiation times and characteristics of primary culture of squamous cell cancer of patients)</li> <li>data_001_pos.csv – manual annotation of gH2AX/53BPI IRIF foci by two experts – cordinates file (in 2D, validation only)</li> </ul> </li> <li>nucleus_segmentation.zip (available in part 1, <a href="https://dx.doi.org/10.5281/zenodo.4067741">https://dx.doi.org/10.5281/zenodo.4067741</a>) Nuclei segmentation Head and neck primocultures immunostained with gH2AX/53BP1, FOVs 237 Training/ 30 Testing/ 10 Validation dataset <ul> <li>data_001.tif – 3channel Z.stack tiff</li> <li>mask_001.tif – respective Z stack mask with manually annotated nucleus mask (manual annotation, training and testing subsets only)</li> <li>data_description.xlsx – description of sample type (2Gy post irradiation times and characteristics of primary culture of squamous cell cancer of patients)</li> </ul> </li> <li>U87.zip and NHDF.zip: Annotated gH2AX/53BP1 foci in cell lines exposed to increasing dose, annotations performed for gH2AX, 53BP1 and colocalized focus separatelly. 679 annotated FOVs for both cell lines. <ul> <li>control.png - RGB control figure showing merge and annotated overlay</li> <li>data_53BP1.tif - TIFF Z-stack, confocal microcopy, 53BP1 channel</li> <li>data_DAPI.tif - TIFF Z-stack, confocal microcopy, DAPI channel</li> <li>data_gH2AX.tif - TIFF Z-stack, confocal microcopy, gH2AX channel</li> <li>labels.json - foci labels for individual channel</li> <li>mask.tif - generated Z-stack of nucleus mask</li> </ul> </li> </ul>
ATM-ESCO2-SMC3 axis promotes 53BP1 recruitment in response to DNA damage and safeguards genome integrity by stabilizing cohesin complex
<p>53BP1 is primarily known as a key regulator in DNA double-strand break (DSB) repair. However, the mechanism of DSB-triggered cohesin modification-modulated chromatin structure on the recruitment of 53BP1 remains largely elusive. Here we identified acetyltransferase ESCO2 as a regulator for DSB-induced cohesin-dependent chromatin structure dynamics, which promotes 53BP1 recruitment. Mechanistically, in response to DNA damage, ATM phosphorylates ESCO2 S196 and T233. MDC1 recognizes phosphorylated ESCO2 and recruits ESCO2 to DSB sites. ESCO2-mediated acetylation of SMC3 stabilizes cohesin complex conformation and regulates the chromatin structure at DSB breaks, which is essential for the recruitment of 53BP1 and the formation of 53BP1 microdomains. Furthermore, depletion of ESCO2 in both colorectal cancer cells and xenografted nude mice sensitizes cancer cells to chemotherapeutic drugs. Collectively, our results reveal a molecular mechanism for the ATM-ESCO2-SMC3 axis in DSB repair and genome integrity maintenance with a vital role in chemotherapy response in colorectal cancer.</p>
ATM-ESCO2-SMC3 axis promotes 53BP1 recruitment in response to DNA damage and safeguards genome integrity by stabilizing cohesin complex
<p>53BP1 is primarily known as a key regulator in DNA double-strand break (DSB) repair. However, the mechanism of DSB-triggered cohesin modification-modulated chromatin structure on the recruitment of 53BP1 remains largely elusive. Here we identified acetyltransferase ESCO2 as a regulator for DSB-induced cohesin-dependent chromatin structure dynamics, which promotes 53BP1 recruitment. Mechanistically, in response to DNA damage, ATM phosphorylates ESCO2 S196 and T233. MDC1 recognizes phosphorylated ESCO2 and recruits ESCO2 to DSB sites. ESCO2-mediated acetylation of SMC3 stabilizes cohesin complex conformation and regulates the chromatin structure at DSB breaks, which is essential for the recruitment of 53BP1 and the formation of 53BP1 microdomains. Furthermore, depletion of ESCO2 in both colorectal cancer cells and xenografted nude mice sensitizes cancer cells to chemotherapeutic drugs. Collectively, our results reveal a molecular mechanism for the ATM-ESCO2-SMC3 axis in DSB repair and genome integrity maintenance with a vital role in chemotherapy response in colorectal cancer.</p>
Annotated DNA Double Strand Break Ionizing Radiation-Induced Foci (gH2AX 53BP1) Confocal Microscopy, pt. 1
<p><strong>Summary</strong></p> <p>Dataset of confocal microscopy data of cells exposed to gamma-irradiation and immunostained with gH2AX and 53BP1.</p> <ul> <li>Nuclei segmentation Head and neck primocultures immunostained with gH2AX/53BP1, Training/Testing/Validation dataset (nucleus_segmentation.zip)</li> <li>IRIF Foci: Head and neck primocultures immunostained with gH2AX/53BP1, Training/Testing/Validation dataset. (foci_detection.zip)</li> <li>Cell lines: U-87 and NHDF Cells exposed to 0.5-8 Gy 30 min and 8h post irradiation - confocal microscopy data of gH2AX/53BP1/DAPI annotated for gH2AX, 53BP1 and colocalized foci separately (cell_lines_U87.zip and NHDF.zip part 2 of dataset, available at <a href="https://dx.doi.org/10.5281/zenodo.5549971">10.5281/zenodo.5549971</a>). </li> <li><strong>Code</strong>: the code is available at <a href="https://github.com/tomasvicar/DeepFoci">https://github.com/tomasvicar/DeepFoci</a></li> <li><strong>Preprint: </strong>Vicar et al, DeepFoci: Deep Learning-Based Algorithm for Fast Automatic Analysis of DNA Double Strand Break Ionizing Radiation-Induced Foci, <a href="https://doi.org/10.1101/2020.10.07.321927">10.1101/2020.10.07.321927</a></li> <li><strong>Publication: </strong>Vicar et al, TBA</li> </ul> <p><strong>Materials and methods</strong></p> <p><em>Dataset</em></p> <p>Following cells were used:</p> <p>1) The training/validation/testing datasets was based on patient-derived primary cell cultures prepared from spinocellular tumors and morphologically normal tissues adjacent to the tumor taken from patients suffering from head and neck cancer. The dataset was divided into two subsets: one for training, validation and testing the nucleus segmentation (237/10/30 fields of view (FOVs), respectively) and one for training, validation and testing the focus segmentation (239/60/100 FOVs). The dataset consisted of several cell types: a) tumor cells, b) tumor-associated fibroblasts, and c) cells from morphologically normal tissues. All cell types were fixed at different periods of time (0 (non-irradiated control), 0.5, 8 or 24 h PI) after exposure to 2 Gy of gamma-rays. The representation of cells in two subsets with respect to the cell type and post-irradiation time (i.e., DSB repair duration) was random.</p> <p>2) The evaluation dataset was used to assess the robustness of segmentation procedures. It was composed of multiple types of differently treated cells in order to represent a highly challenging dataset maximally reflecting high biological and technical variability between samples, as it may appear in research or clinical practice. The dataset contained a) mesenchymal NHDF fibroblasts coming from a standard permanent cell line, b) radioresistant U-87 glioblastoma cells coming from a standard permanent cell line, c) tumor cells (CD90-) and tumor-associated fibroblasts (CD90+) prepared as a primary culture from a spinocellular tumors of patients (different from dataset 1) suffering from a head and neck cancer, and d) cells prepared as primary cultures from morphologically normal tissue adjacent to tumors of involved head and neck cancer patients. NHDF and U-87 cells received 0.5, 0, 1, 2, 4 and 8 Gy of gamma-rays and were fixed at 30 min and 8 h post-irradiation, while the primary cultures were only exposed to the dose of 2 Gy (for a limited amount of the cell material) and fixed at 0 (non-irradiated control), 0.5, 8 or 24 h post-irradiation times.</p> <p><em>Gamma irradiation</em></p> <p>The cells were irradiated at the Institute of Biophysics, Czech Academy of Sciences, Brno, Czech Republic in a following schemes: (a) patient-derived primoculture was irradiated with a single dose of 2 Gy (D = 1 Gy/min) of gamma-rays (60Co, Chisostat, Chirana, CR) , (b) U-87 and NHDF cells were irradiated with doses 0.5-8 Gy (D = 1 Gy/min). Cells were irradiated in RPMI 1640 medium (37 °C, normal atmosphere). Confocal microscopy of gammaH2AX and 53BP1 foci immunodetection was consequently performed.</p> <p><em>Fluorescent staining</em></p> <p>DNA double strand breaks (DSBs) were quantified in different periods of time post-irradiation (30 min, 8h and 24h post irradiation) by means of $\gamma$H2AX and 53BP1 foci immunodetection combined with confocal microscopy. For details see \cite{falk2007chromatin}.</p> <p><em>Confocal microscopy</em></p> <p>The microscopy of samples was performed at the Institute of Biophysics, Czech Academy of Sciences, Brno, Czech Republic. Leica DM RXA microscope (equipped with DMSTC motorized stage, Piezzo z-movement, MicroMax CCD camera, CSU-10 confocal unit and 488, 562, and 714 nm laser diodes with AOTF) was used for acquiring detailed cell images (100× oil immersion Plan Fluotar lens, NA 1.3). Total 50 Z slices was captured with Z step size 0.3 μm.</p> <p><strong>File description</strong></p> <p>all files are compressed hyperstack tiffs (50 Z slices and 3 fluorescent channels, XYCZ order), 100x magnification</p> <ul> <li>foci_detection.zip: IRIF Foci: Head and neck primocultures immunostained with gH2AX/53BP1, Training/Testing/Validation dataset: FOVs 240/100/120 files for training, testing, and validation, organisation: <ul> <li>data_001.tif – 3channel Z.stack tiff</li> <li>mask_001.tif – respective Z stack mask with single points per IRIF focus (manual annotation, training and testing subsets only)</li> <li>data_description.xlsx – description of sample type (2Gy post irradiation times and characteristics of primary culture of squamous cell cancer of patients)</li> <li>data_001_pos.csv – manual annotation of gH2AX/53BPI IRIF foci by two experts – cordinates file (in 2D, validation only)</li> </ul> </li> <li>nucleus_segmentation.zip Nuclei segmentation Head and neck primocultures immunostained with gH2AX/53BP1, FOVs 237 Training/ 30 Testing/ 10 Validation dataset <ul> <li>data_001.tif – 3channel Z.stack tiff</li> <li>mask_001.tif – respective Z stack mask with manually annotated nucleus mask (manual annotation, training and testing subsets only)</li> <li>data_description.xlsx – description of sample type (2Gy post irradiation times and characteristics of primary culture of squamous cell cancer of patients)</li> </ul> </li> <li>U87.zip and NHDF.zip: Annotated gH2AX/53BP1 foci in cell lines exposed to increasing dose, annotations performed for gH2AX, 53BP1 and colocalized focus separatelly. 679 annotated FOVs for both cell lines (part 2 of dataset, available at <a href="https://dx.doi.org/10.5281/zenodo.5549971">10.5281/zenodo.5549971</a>). <ul> <li>control.png - RGB control figure showing merge and annotated overlay</li> <li>data_53BP1.tif - TIFF Z-stack, confocal microcopy, 53BP1 channel</li> <li>data_DAPI.tif - TIFF Z-stack, confocal microcopy, DAPI channel</li> <li>data_gH2AX.tif - TIFF Z-stack, confocal microcopy, gH2AX channel</li> <li>labels.json - foci labels for individual channel</li> <li>mask.tif - generated Z-stack of nucleus mask</li> </ul> </li> </ul>
UTX and 53BP1 co-regulate genetic programs for neural differentiation of human embryonic stem cells [mouse RNA-seq]
GEO Series GSE120333. Mus musculus. 8 samples. Type: Expression profiling by high throughput sequencing.
UTX and 53BP1 co-regulate genetic programs for neural differentiation of human embryonic stem cells [ChIP-seq]
GEO Series GSE108114. Homo sapiens. 32 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
SHLD1 is dispensable for 53BP1-dependent V(D)J recombination but critical for productive class switch recombination
GEO Series GSE202567. Mus musculus. 18 samples. Type: Other.
UTX and 53BP1 co-regulate genetic programs for neural differentiation of human embryonic stem cells [RNA-seq]
GEO Series GSE108115. Homo sapiens. 27 samples. Type: Expression profiling by high throughput sequencing.
Regulated the AEJ -mediated V(D)J recombination by 53BP1 and ATM
GEO Series GSE242952. Mus musculus. 510 samples. Type: Other.
53BP1 loss elicits cGAS-STING-dependent antitumor immunity in ovarian and pancreatic cancer
GEO Series GSE237615. Mus musculus. 16 samples. Type: Expression profiling by high throughput sequencing.
ATM and 53BP1 regulate alternative end joining-mediated V(D)J recombination
GEO Series GSE246239. Mus musculus. 42 samples. Type: Other.
UTX and 53BP1 co-regulate genetic programs for neural differentiation of human embryonic stem cells
GEO Series GSE108116. Homo sapiens; Mus musculus. 67 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
Expression data of ATM, ATR, CHK1, CHK2, and 53BP1 shRNA knockdown and control shRNA in MCF-10A cells
GEO Series GSE54268. Homo sapiens. 36 samples. Type: Expression profiling by array.
53BP1 integrates DNA repair and p53-dependent cell fate decisions via distinct mechanisms
GEO Series GSE84986. Homo sapiens. 36 samples. Type: Expression profiling by high throughput sequencing.
Study Evaluating DNA Double-strand Breaks (DSBs) REpair Factors (POLQ, Shieldin Complex and 53BP1) Expression as Biomarker of PARP Inhibitor Resistance in Patients With Deleterious Germline Mutation i
ClinicalTrials.gov study NCT05378204. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Transient Inhibition of 53BP1 Increases the Frequency of Targeted Integration in Human Hematopoietic Stem and Progenitor Cells
GEO Series GSE246766. Homo sapiens. 12 samples. Type: Other.
PALB2 and 53BP1 govern post-resection homologous recombination DNA repair
GEO Series GSE299657. Mus musculus. 3 samples. Type: Other.
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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.