Find research datasets worth reusing

opencc-by-4.0Feb 2019View details →

Confocal microscopy of gH2AX and 53BP1 DNA repair foci of cells exposed to gamma-irradiation, pt. 2/3

Summary Dataset of confocal microscopy data of cells exposed to gamma-irradiation and immunostained with gH2AX and 53BP1. <ul> <li>Part 1/3: 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>Part 2/3 (this dataset): 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>Part 3/3: 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>Code: the code is available at <a href="https://github.com/tomasvicar/LearnFoci">https://github.com/tomasvicar/LearnFoci</a></li> </ul> Materials and methods Dataset 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 Svobodova et al, 2017, (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. 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. Gamma irradiation 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. Fluorescent staining 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}. Confocal microscopy 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. File description all files are compressed hyperstack tiffs (50 Z slices and 3 fluorescent channels, XYCZ order), 100x magnification <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>

opencc-by-nc-sa-4.0Feb 2017View details →

Data for 'Comparative Analysis of Single-Cell RNA Sequencing Methods'

Raw sequencing data to "Comparative Analysis of Single-Cell RNA Sequencing Methods".  https://www.ncbi.nlm.nih.gov/pubmed/28212749   In addition to the GEO submission https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE75790, you can find here raw bam files for UMI-methods tagged with cell barcode and UMI sequences. MD5 checksum: f10825509952fffd9c4dc0c1dcb9eb8e

opencc-by-4.0Feb 2019View details →

Confocal microscopy of gH2AX and 53BP1 DNA repair foci of cells exposed to gamma-irradiation, pt. 1/3

Summary Dataset of confocal microscopy data of cells exposed to gamma-irradiation and immunostained with gH2AX and 53BP1. <ul> <li>Part 1/3 (this dataset): 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>Part 2/3: 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>Part 3/3: 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>Code: the code is available at <a href="https://github.com/tomasvicar/LearnFoci">https://github.com/tomasvicar/LearnFoci</a></li> </ul> Materials and methods Dataset 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 Svobodova et al, 2017, (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. 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. Gamma irradiation 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. Fluorescent staining 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}. Confocal microscopy 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. File description all files are compressed hyperstack tiffs (50 Z slices and 3 fluorescent channels, XYCZ order), 100x magnification <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>

opencc-by-4.0Dec 2017View details →

Chromatin regulation by Histone H4 acetylation at Lysine 16 during cell death and differentiation in the myeloid compartment

Histone H4 acetylation at Lysine 16 (H4K16ac) is a key epigenetic mark involved in gene regulation, DNA repair and chromatin remodeling, and though it is known to be essential for embryonic development, its role during adult life is still poorly understood. Here we show that this lysine is massively hyperacetylated in peripheral neutrophils. Genome-wide mapping of H4K16ac in terminally differentiated blood cells, along with functional experiments, supported a role for this histone post-translational modification in the regulation of cell differentiation and apoptosis in the hematopoietic system. Furthermore, in neutrophils, H4K16ac was enriched at specific DNA repeats. These DNA regions presented an accessible chromatin conformation and were associated with the cleavage sites that generate the 50 kb DNA fragments during the first stages of programmed cell death. Our results thus suggest that H4K16ac plays a dual role in myeloid cells as it not only regulates differentiation and apoptosis, but it also exhibits a non-canonical structural role in poising chromatin for cleavage at an early stage of neutrophil cell death.

opencc-by-4.0Jan 2019View details →

Expression and purification of HTT79-3144 with and without HAP40 from Sf9 Insect cells - 2019/01/28

Project: Biophysical investigation of purified HTT protein samples Experiment: Expression and purification of HTT79-3144 with and without HAP40 from Sf9 Insect cells Date completed: 2019/01/28 Rationale: HTT lacking the unstructured region of exon1 (aa. 1-78 which are not resolved in the cryoEM model PDB ID 6EZ8) may serve as a useful control when determining exon1-dependent functionality of the HTT protein. Apo and HAP40-bound HTT79-3144 will be produced from Sf9 insect cell expression system.

opencc-by-4.0Mar 2019View details →

Supplemental Figures S1-S8: Direct CD137 costimulation of CD8 T cells promotes retention and innate-like function within nascent atherogenic foci

Supplemental Figures and Table S1-S8 for "Direct CD137 costimulation of CD8 T cells promotes retention and innate-like function within nascent atherogenic foci" H-00088-2019, to the American Journal of Physiology-Heart and Circulatory Physiology.

opencc-by-4.0Dec 2018View details →

Multi-angle light scattering (MALS) analysis of HTT1-3144 Q54 HAP401-371 samples purified from Sf9 insect cells - 2018/12/03

Project: Biophysical investigation of purified HTT protein samples Experiment: Multi-angle light scattering (MALS) analysis of HTT1-3144 Q54 HAP401-371samples purified from Sf9 insect cells Date completed: 2018/12/03 Rationale: Apo HTT1-3144 Q23 and HTT1-3144 Q23 HAP401-371complex samples have been analysed by MALS revealing HTT-HAP40 complex samples to be monodisperse. PolyQ expanded HTT constructs have been expressed as HAP40 complexes but the monodispersity has not been assessed beyond analytical gel filtration.

opencc-by-4.0May 2019View details →

Supplemental Videos for: Association of SLC52A3a [p. L267P] and [p. T278M] with riboflavin transportation in esophageal cancer cells

Supplemental data Supplemental Video S1 showing motility of GFP-SLC52A3a-WT containing vesicles in KYSE150 R+ cells;  Supplemental Video S2 showing motility of GFP-SLC52A3a-WT containing vesicles in KYSE150 R- cells;  Supplemental Video S3 showing motility of GFP-SLC52A3a-L267P containing vesicles in KYSE150 R+ cells; Supplemental Video S4 showing motility of GFP-SLC52A3a-L267P containing vesicles in KYSE150 R- cells; Supplemental Video S5 showing motility of GFP-SLC52A3a-T278M containing vesicles in KYSE150 R+ cells; Supplemental Video S6 showing motility of GFP-SLC52A3a-T278M containing vesicles in KYSE150 R- cells; Supplemental Video S7 showing motility of GFP-SLC52A3a-L267/T278M containing vesicles in KYSE150 R+ cells; Supplemental Video S8 showing motility of GFP-SLC52A3a-L267/T278M containing vesicles in KYSE150 R- cells.

Influence of environmental conditions on the fusion of cationic liposomes with living mammalian cells

Lipid-based nanoparticles, also called vesicles or liposomes, can be used as carriers for drugs or many types of biological macromolecules including DNA and proteins. Efficiency and speed of cargo delivery are especially high for carrier vesicles that fuse with the cellular plasma membrane. This occurs for lipid mixture containing equal amounts of the cationic lipid DOTAP and a neutral lipid with an additional few percent of an aromatic substance. The fusion ability of such particles depends on lipid composition with phosphoethanolamine (PE) lipids favoring fusion and phosphatidyl-choline (PC) lipids endocytosis. Here we examined the effects of temperature, ionic strength, osmolality, and pH on fusion efficiency of cationic liposomes with Chinese hamster ovary (CHO) cells. The phase state of liposomes was analyzed by small angle neutron scattering (SANS). Our results showed that PC containing lipid membranes were organized in the lamellar phase. Here, fusion efficiency depended on buffer conditions and remained vanishingly small at physiological conditions. In contrast, SANS indicated the coexistence of very small (~ 50 nm) objects with larger, most likely lamellar structures for PE containing lipid particles. The fusion of such particles to cell membranes occurred with very high efficiency at all buffer conditions. We hypothesize that the altered phase state resulted in a highly reduced energetic barrier against fusion.

Optimisation of viability assay for DIPG patient-derived cell lines

Evaluation of the efficacy of M4K compounds in DIPG patient-derived cell lines is essential before any promising compounds can be further tested in mouse xenograft models. This approach can aid in narrowing down clinical compound candidates and reduce the time, resources and animal sacrifice needed downstream. A robust and efficient readout for the changes in the viability of the DIPG cells needs to be established before it can be used to evaluate the M4K compounds. In addition, the amount of cells to be seeded at the beginning of the experiment has to be optimised to avoid overcrowding and starvation of the cells after extended culture times. Overcrowding and starvation will lead to increased cell death and prevent accurate estimation of the potency of M4K compounds (EC50).

Mapping cis-regulatory chromatin contacts in neural cells links neuropsychiatric disorder risk variants to target genes

ATAC-seq peaks are in narrowPeak format. RNA-seq results are organized according to cell type. The normalized RPKM is reported for each gene in GENCODE 19. All data was mapped to hg19.

Ensemble and single cell data for primary Ovis Aries pulmonary artery endothelial cells response to IGF-1 administration

Data for IGF-1 administration of healthy and persistent pulmonary hypertension of the newborn primary Ovis Aries pulmonary artery endothelial cells. Ensemble.zip: Dose-response to IGF-1 Proliferation Western blots for VEGF and eNOS IGF-1R and mTOR inhibition Branch points in tube formation assay IF.zip: Cellprofiler 3.1 analysis of snapshot data for the time course of IGF-1 administration with nuclei, actin, VEGF, and eNOS Translation.zip: CellProfiler 3.1 analysis of snapshot data for the time course of IGF-1 administration with nuclei and total protein production

Movie files: Actin dynamics and the Bmp pathway drive apical extrusion of proepicardial cells.

The epicardium, the outer mesothelial layer enclosing the myocardium, plays key roles in heart development and regeneration. During embryogenesis it arises from the proepicardium (PE), a cell cluster that appears in the dorsal pericardium (DP) close to the venous pole of the heart. Little is known about how the PE emerges from the pericardial mesothelium. Using the zebrafish model and a combination of genetic tools, pharmacological agents and quantitative in vivo imaging, we reveal that a coordinated collective movement of DP cells drives PE formation. We found that BMP signaling and the actomyosin cytoskeleton promote constriction of the DP, which enabled PE cells to extrude apically. We provide evidence that cell extrusion, which has been described in the elimination of unfit cells from epithelia and the emergence of hematopoietic stem cells, is also a mechanism for PE cells to exit an organized mesothelium and fulfil the developmental fate to form a new tissue layer, the epicardium.

ROS-Specific Huntingtin Interactions: Chromatin Retention of Huntingtin in PARP KO Cells

Huntingtin chromatin retention in response to oxidative stress in wild type, PARP1 knockout, PARP2 knockout, and PARP1/PARP2 knockout RPE1 cells.

ROS-Specific Huntingtin Interactions: Poly ADP Ribose Levels in STHdh Cells

Comparison of poly ADP ribose levels in Q7/Q7 versus Q111/Q111 STHdh cells in response to oxidative stress.

Attenuation of chronic T cell responses through constitutive COX2-dependent prostanoid synthesis by lymph node fibroblasts

Raw data (in microsoft excel format) which were used to generate the figures in this manuscript. One worksheet per figure.

The Pseudomonas aeruginosa T6SS delivers a periplasmic toxin that disrupts bacterial cell morphology - 6H56

VgrG2b X-ray diffraction data for PDB entry 6H56. => VgrG2b_p3: Native protein, one dataset => VgrG2b_SeMet: Se-Met protein, four datasets Data were collected at beamline I02 of Diamond Light Source on 24 Jun 2013 (VgrG2b_p3) and at beamline I04 of Diamond Light Source on 17 Apr 2014 (VgrG2b_SeMet).

Supporting data for "Cellulose separators with integrated carbon nanotube interlayers for lithium-sulfur batteries: an investigation into the complex interplay between cell components"

This is the dataset of electrochemical experiments for our publication "Cellulose separators with integrated carbon nanotube interlayers for lithium-sulfur batteries: an investigation into the complex interplay between cell components". This archive contains the raw data and scripts written in R used in the analysis and presentation of the results in this manuscript. Abstract for the manuscript: This work aims to address two major roadblocks in the development of lithium-sulfur (Li-S) batteries: the inefficient deposition of Li on the metallic Li electrode and the parasitic “polysulfide redox shuttle”. These roadblocks are here approached, respectively, by the combination of a cellulose separator with a cathode-facing conductive porous carbon interlayer, based on their previously reported individual benefits. The cellulose separator increases cycle life by 33%, and the interlayer by a further 25%, in test cells with positive electrodes with practically relevant specifications and a relatively low electrolyte/sulfur (E/S) ratio. Despite the prolonged cycle life, the combination of the interlayer and cellulose separator increases the polysulfide shuttle current, leading to reduced Coulombic efficiency. Based on XPS analyses, the latter is ascribed to a change in the composition of the solid electrolyte interphase (SEI) on Li. Meanwhile, electrolyte decomposition is found to be slower in cells with cellulose-based separators, which explains their longer cycle life. These counterintuitive observations demonstrate the complicated interactions between the cell components in the Li-S system and how strategies aiming to mitigate one unwanted process may exacerbate another. This study demonstrates the value of a holistic approach to the development of Li-S chemistry. Manuscript preprint <a href="http://dx.doi.org/10.26434/chemrxiv.8835728">available at ChemRxiv</a> (pending approval as of 9/7/19).

Different methods to evaluate the effects of M4K compounds on DIPG patient-derived cell lines

Aside from determining the optimal numbers of DIPG cells to be seeded for viability assay, it is also important to validate that measurements using CellTiter Glo are in agreement with other methods of determining cell viability. For my blog post about this experiment, please visit my opennotebook page. https://openlabnotebooks.org/different-methods-to-evaluate-the-effects-of-m4k-compounds-on-dipg-patient-derived-cell-lines/

Data for "Layer 4 of mouse neocortex differs in cell types and circuit organization between sensory areas"

Data for "Layer 4 of mouse neocortex differs in cell types and circuit organization between sensory areas". Preprint: https://www.biorxiv.org/content/10.1101/507293v2. Raw sequencing data is available at https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE134378.