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&nbsp;<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&nbsp;<a href="https://doi.org/10.5281/zenodo.2572450">10.5281/zenodo.2572450</a>.&nbsp;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&nbsp;<a href="https://doi.org/10.5281/zenodo.2576241">10.5281/zenodo.2576241</a>.&nbsp;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&nbsp;<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 &nbsp;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&rsquo;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 &deg;C and 50% CO2 in humidified atmosphere up to 50% confluence. U-87 were grown in Eagle&#39;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 &deg;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 &nbsp;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&times; oil immersion Plan Fluotar lens, NA 1.3). Total 50 Z slices was captured with Z step size 0.3 &mu;m.</p> <p><strong>File description</strong></p> <p>all files are&nbsp;compressed hyperstack tiffs (50 Z slices and 3 fluorescent channels, XYCZ order), 100x magnification</p> <ul> <li>Confocal_NHDF_cells_IR_1-4Gy.zip:&nbsp;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>