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1,853 results for “cell culture”
Data from: Immune Transcriptional Response in Head Kidney Primary Cell Cultures Isolated from the Three Most Important Species in Chilean Salmonids Aquaculture.
<p>Data from Immune Transcriptional Response in Head Kidney Primary Cell Cultures Isolated from the Three Most Important Species in Chilean Salmonids Aquaculture. Files in .JBN and .xlsx format</p>
Virtual Screening and Testing of GSK-3 Kinase Inhibitors Using human SH-SY5Y Neuronal cells Expressing Tau Folding Reporter and Mouse Hippocampal Primary Neuron Culture Under Tau Cytotoxicity
<p>Supplementary Figure S1. for IJMS</p>
In situ monitoring reveals cellular environmental instabilities in human pluripotent stem cell culture
<p>Mammalian cell cultures are a keystone resource in biomedical research, but the results of published experiments often suffer from reproducibility challenges. This has led to a focus on the influence of cell culture conditions on cellular responses and reproducibility of experimental findings. Here, we perform frequent in situ monitoring of dissolved O<sub>2</sub> and CO<sub>2</sub> with optical sensor spots and contemporaneous evaluation of cell proliferation and medium pH in standard batch cultures of three widely used human somatic and pluripotent stem cell lines. We collate data from the literature to demonstrate that standard cell cultures consistently exhibit environmental instability, indicating that this may be a pervasive issue affecting experimental findings. Our results show that <i>in vitro</i> cell cultures consistently undergo large departures of environmental parameters during standard batch culture. These findings should catalyze further efforts to increase the relevance of experimental results to the in vivo physiology and enhance reproducibility.</p>
Raw gel and membrane figures associated with the publication "Iron-loaded deferiprone can support full hemoglobinization of cultured red blood cells"
<p>Raw gel and membrane figures associated with the publication <strong>Iron-loaded deferiprone can support full hemoglobinization of cultured red blood cells</strong>.</p> <p> </p> <p><strong>For Figure 1a:</strong></p> <p>Raw uncropped image of the gel run with samples combining apotransferrin with iron chelators. After staining with Coomassie, gel was scanned in an Epson V500 scanner (full color, 1200 dpi, bit depth = 24).</p> <p> </p> <p><strong>For Figure 3:</strong></p> <p>Raw uncropped images of the membranes obtained from western blots of cultured erythroblasts derived from three different donors, showing the expression level of proteins involved in iron metabolism regulation (ferritin, transferrin receptor, total EIF2, phospho-EIF2). Actin was used as housekeeping protein for relative quantification of protein abundance for further analysis.</p> <p>After staining, membranes were scanned in an Epson V500 scanner (full color, 1200 dpi, bit depth = 24).</p> <p>For all membranes, the loading order is the same:</p> <p>- <strong>Day 0:</strong> 1000 μg/mL holotransferrin</p> <p>- <strong>Day 0:</strong> 100 μg/mL holotransferrin</p> <p>- <strong>Day 0:</strong> 100 μg/mL holotransferrin + 52 μM iron-loaded deferiprone</p> <p>- <strong>Day 1:</strong> 52 μM iron-loaded deferiprone</p> <p>- <strong>Day 1:</strong> 1000 μg/mL apotransferrin</p> <p>- <strong>(empty lane)</strong></p> <p>- <strong>Day 1:</strong> 1000 μg/mL holotransferrin</p> <p>- <strong>Day 1:</strong> 100 μg/mL holotransferrin</p> <p>- <strong>Day 1:</strong> 100 μg/mL holotransferrin + 52 μM iron-loaded deferiprone</p> <p>- <strong>Day 1:</strong> 52 μM iron-loaded deferiprone</p> <p>- <strong>Day 1:</strong> 1000 μg/mL apotransferrin</p> <p>- <strong>(empty lane)</strong></p> <p>- <strong>Day 2:</strong> 1000 μg/mL holotransferrin</p> <p>- <strong>Day 2:</strong> 100 μg/mL holotransferrin</p> <p>- <strong>Day 2:</strong> 100 μg/mL holotransferrin + 52 μM iron-loaded deferiprone</p> <p>- <strong>Day 2:</strong> 52 μM iron-loaded deferiprone</p> <p>- <strong>Day 2:</strong> 1000 μg/mL apotransferrin</p> <p>More details on the protocol for western blot available in the manuscript at https://doi.org/10.1101/2021.08.02.454758</p> <p> </p> <p><strong>For Figure 4:</strong></p> <p>Raw uncropped images of the membranes obtained from western blots of cultured erythroblasts derived from two different donors with different iron supplementations (no hTf or Def, 52 μM iron-loaded deferiprone, or 300 μg/mL holotransferrin), showing the phosphorylation level of STAT5 upon withdrawal of erythropoietin (Epo) (3 hours) and restimulation with 0.2 or 1.0 U/mL Epo.</p> <p>After staining, membranes were scanned in an Epson V500 scanner (full color, 1200 dpi, bit depth = 24).</p> <p>For both membranes, the loading order is the same:</p> <p>- <strong>Lane 1:</strong> cells cultured without hTf nor Def, and no Epo restimulation</p> <p>- <strong>Lane 2:</strong> cells cultured with 52 μM iron-loaded deferiprone, and no Epo restimulation</p> <p>- <strong>Lane 3:</strong> cells cultured with 300 μg/mL holotransferrin, and no Epo restimulation</p> <p>- <strong>Lane 4:</strong> cells cultured without hTf nor Def, and restimulation with 0.2 U/mL Epo.</p> <p>- <strong>Lane 5:</strong> cells cultured with 52 μM iron-loaded deferiprone, and restimulation with 0.2 U/mL Epo.</p> <p>- <strong>Lane 6:</strong> cells cultured with 300 μg/mL holotransferrin, and restimulation with 0.2 U/mL Epo.</p> <p>- <strong>Lane 7:</strong> cells cultured without hTf nor Def, and restimulation with 1.0 U/mL Epo.</p> <p>- <strong>Lane 8:</strong> cells cultured with 52 μM iron-loaded deferiprone, and restimulation with 1.0 U/mL Epo.</p> <p>- <strong>Lane 9:</strong> cells cultured with 300 μg/mL holotransferrin, and restimulation with 1.0 U/mL Epo.</p>
Ectopic expression of murine CD163 enables cell-culture isolation of lactate dehydrogenase-elevating (LDV) virus 63 years after its discovery
<p><span>Arteriviruses are RNA viruses related to coronaviruses but have not yet been associated with human infection. A murine arterivirus (lactate dehydrogenase-elevating virus, LDV) was first described in 1960 and quickly became a promising model for understanding immune failure due to its unique ability to persist in immunocompetent adult mice. However, inability to culture LDV <em>in vitro</em> ultimately limited this system. Here, we demonstrate that the macrophage marker CD163 is essential for LDV infection. Expression of the murine homolog (mCD163) in otherwise mCD163-negative cell lines from mice and nonhuman primates enables productive LDV infection, creating the first immortalized cell-culture system. We also show that mCD163-knockout mice are completely resistant to LDV infection. These findings advance LDV as a model of arterivirus infection viral persistence and add to a growing body of literature suggesting that CD163 utilization is a broad feature of arteriviruses.</span></p>
Machine Learning Tools for Peptide Bioactivity Evaluation Implications for Cell Culture Media Optimization and the Broader Cultivated Meat Industry
Open the record for dataset details and reuse information.
Nasal organoids as optimal models for studying structure and function of primary nasal epithelial cell cultures - DIA-MS Dataset
Open the record for dataset details and reuse information.
Report: Culturing patient leukemic cells
<p>A summary of our culturing and immunophenotyping of primary leukemic cells from AML patients.</p>
Supplementary Videos S1-S2 3D co-culture spheroid formation containing A498-ST cells
<p><strong>Supplementary Videos S1-S2</strong></p> <p><strong>3D co-culture spheroid formation containing A498-ST cells </strong></p> <p>Representative movies (<strong>S1</strong>, bright field and <strong>S2,</strong> fluorescence stained) recorded for 24 hours of an A498-ST 3D co-culture capturing the kinetic formation of a 3D spheroid. 3D co-cultures harbor 70% tumor cells (A498-ST, green), 20% fibroblasts (NHDFα, blue) and 10% endothelial cells (ECRF24, red). Scalebar represents 1000 µm. </p>
Raw data for the article "In vitro culture of leukemic cells in collagen scaffolds and carboxymethylcellulose-polyethylene glycol gel"
<p>Uncropped original micrographs and raw numerical data of figures and tables from the article submitted to PeerJ. </p>
Microscopy images of the DNA and RNA polymerase II distribution inside nuclei of cell cultures obtained from pluripotent zebrafish embryos
<p><strong>Image data description</strong></p> <p>Color channels in the image data:</p> <ol> <li>First channel: DNA (Hoechst 33342)</li> <li>Second channel: Pol II Ser2P (Elongating RNA polymerase II, indirect immunofluorescence, STAR RED)</li> <li>Third channel: Pol II Ser5P (Recruited RNA polymerase II, indirect immunofluorescence, Alexa 594)</li> </ol> <p><strong>Sample description</strong></p> <p>Praimary cell cultures were prepared from pluripotent zebrafish embryos were collected at the sphere stage of development, treated with chemical inhibitors of transcription (Control, 500 mM Flavopiridol, 500 mM Triptolide, all for 30 min) and fixed overnight (2% formaldehyde in culutre media, 30 min, room temperature; followed by 8% formaldehyde for 15 min at room temperature). RNA polymerase in the recruited state (Pol II Ser5P) and the elongating state (Pol II Ser2P) were labeled by indirect immunofluorescence (permeabilization 0.5% Triton X-100 in PBS 15 min room temperature, 30 min blocking 4% BSA in PBST, rat IgG anti-Pol II Ser5P & rabbit IgG anti-Pol II Ser2P in 4% BSA in PBST overnight 4°C, anti-rat Alexa 594 & anti-rabbit STAR RED in 4% BSA in PBST overnight 4°C). Mounted in VectaShield H-1000 with 2 µM Hoechst 33342 added for fluorescent DNA labeling. Scan of lab book page is included in the repository.</p> <p>The data set contains images obtained from two samples for each condition.</p> <p><strong>Imaging</strong></p> <p>Microscopy images acquired using VisiTech iSIM with dual camera setup. Objective Nikon CFI SR HP Apo<br> TIRF 100XAC Oil, color channels acquired in a sequence to reduce overlap (DNA + Ser2P acquired simultaneously on two camerase, Ser5P acquired after on a single camera), z-stack settings optimized to ensure reliable xyz alignment of channels. Imags were cropped to the region with best signal and resolution in the DNA channel, same region used throughout the entire dataset. all imaging settings were kept unchanged over the course of acquisition, all images acquired in a single session of 4 hours.</p> <p><strong>Advice for image processing</strong></p> <p>Images can be loaded for processing with the OME bioformats importer. An import script for MatLab is available through the Hilbert lab: https://github.com/lhilbert/NuclearObjects_ImageAnalysis</p> <p><strong>Author contributions</strong></p> <p>AN & MS provided embryos, carried out cell culture, and prepared samples, LH performed microscopy</p>
Culturing Patient-Derived Malignant Hematopoietic Stem Cells in Engineered and Fully Humanized 3D Niches
<p>Data underlying the figures in the publication “Culturing patient-derived malignant hematopoietic stem cells in engineered and fully humanized 3D niches”, published in <em>PNAS,</em><em> <strong>2021</strong>, 118 (40) e2114227118.</em></p> <p><em>DOI: 10.1073/pnas.2114227118</em></p> <p>Table of contents:</p> <p><strong>1. AML data_Gene expression</strong>: qPCR data related to AML samples.</p> <p><strong>2. AML data_Protein</strong>: Luminex data related to AML samples.</p> <p><strong>3. AML data_Supernatant vs Niche</strong>: FACS data comparing AML cells in the supernatant and niche compartments.</p> <p><strong>4. AML data_Supernatant</strong>: FACS data showing AML cells in the supernatant along the time.</p> <p><strong>5. Chemotherapy_2D_FACS</strong>: FACS data showing leukemic cell viability in 2D.</p> <p><strong>6. Chemotherapy_3D_FACS</strong>: FACS data showing leukemic cell viability in 3D (engineered niches).</p> <p><strong>7. MPN data</strong>: FACS data related to MPN samples.</p> <p><strong>8. SV-N_FACS</strong>: FACS data characterizing SV-N.</p> <p><strong>9. SV-N_Gene expression</strong>: qPCR data characterizing SV-N.</p> <p><strong>10. UCSD-AML1_Niche_FACS</strong>: FACS data showing UCSD-AML1 cells in the niche at final analysis.</p> <p><strong>11. UCSD-AML1_Niche_Gene expression</strong>: qPCR data showing UCSD-AML1 cells in the niche at final analysis.</p> <p><strong>12. UCSD-AML1_Supernatant_FACS</strong>: FACS data showing UCSD-AML1 cells in the supernatant along the time.</p> <p><strong>13. UCSD-AML1_Supernatant_Gene expression</strong>: qPCR data related to UCSD-AML1 cells in the supernatant along the time.</p> <p><strong>14. UCSD-AML1_Supernatant_Protein</strong>: Luminex data related to UCSD-AML1 cells in the supernatant along the time.</p> <p><strong>15. Images engineered niches</strong>: Zip archive containing images of engineered niches.</p>
FIGURE. Myrmecridium schulzeri (IFRD500–012) a, b. Colonies on natural substrate. c–e. Conidiophores with conidia. f, g. Conidiogenous cells with conidia. h–l. Conidia. m Germinating conidia on PDA. n, o. Culture on PDA, n. from front, o. from reverse. Scale bars: c–e, h = 20 μm, m = 10 μm, f, g = 5 μm, i–l = 2 μm. in Yunnan-Guizhou Plateau: a mycological hotspot
FIGURE. Myrmecridium schulzeri (IFRD500–012) a, b. Colonies on natural substrate. c–e. Conidiophores with conidia. f, g. Conidiogenous cells with conidia. h–l. Conidia. m Germinating conidia on PDA. n, o. Culture on PDA, n. from front, o. from reverse. Scale bars: c–e, h = 20 μm, m = 10 μm, f, g = 5 μm, i–l = 2 μm.
Fig. 7. Superimposed 3D in Structure and activity of a novel robust peroxidase from Alkanna frigida cell culture
Fig. 7. Superimposed 3D structure of HRP-C (in brown) on A) 1AP2 and B) POXalf. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
Fig. 6. A in Structure and activity of a novel robust peroxidase from Alkanna frigida cell culture
Fig. 6. A) RMSD and B) RMSF plots obtained from the analysis of MD simulations (120 ns) of POXalf model.
Fig. 5. A in Structure and activity of a novel robust peroxidase from Alkanna frigida cell culture
Fig. 5. A) Approved 3D model of POXalf (residues 61–75 are 80% transparent). B) Topology of helices in 3D structures of POXalf and HRP (PDB:1HCH). C) Stereo environments of distal and proximal Ca ions in POXalf structure.
Fig. 3. A in Structure and activity of a novel robust peroxidase from Alkanna frigida cell culture
Fig. 3. A) The 2-D gel IEF of POXalf. B) Optimal pH of activity, C) optimal temperature of activity, and D) the thermal stability of POXalf in the presence of phenol (●) and guaiacol (▴). The average of triple assays of POXsolution (stored at 4 ◦ C) activity in the presence of phenol on E) day 1 and F) day 720. All the phenol (8.6 mM) alf and guaiacol (5 mM) reactions were carried out in PBS (10 mM) in the presence of constant amounts of POXalf (65.35 nM) and H2O2 (6.76 mM). Constant pH of 7 and 6 (for phenol and guaiacol, respectively) and constant temperature (20 ± 1 ◦ C) were applied when needed. POXwas maintained 10 min at the desired pH and alf temperature prior to the assays for the stability examinations.
Fig. 2. A in Structure and activity of a novel robust peroxidase from Alkanna frigida cell culture
Fig. 2. A) SDS-PAGE of purified POXalf [lane1: Ladder, lane2:HRP, lanes3,4&5: POXalf] stained by Coomassie blue (left) and silver nitrate (right). Chromatograms of POXalf purification on B) size exclusion column [Sephadex G50, pH 6] and C) ion-exchange column [S-Sepharose, pH 6, NaCl 0.2 M]. D) UV–Visible spectrum of purified POXalf. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
Fig. 1. A in Structure and activity of a novel robust peroxidase from Alkanna frigida cell culture
Fig. 1. A) A. frigida callus at the end of a 31- day subculture and B) its corresponding growth profile. C) POX production in the calluses of A. frigida [A.f], Arnebia euchroma [A.e], Lithospermum officinale [L.o], Onosma dasytrichum [O.d], and Nonea caspica [N.c]. D) POX (filled columns) and CAT (dashed columns) activities in the extract of A. frigida callus during a 31-day subculture. The subcultures were carried out on solid MS medium containing kinetin (10 μM), 2,4-D (1 μM), and sucrose (5% w/v) in darkness at 25 ◦ C. See the experimental section for the enzymatic assays conditions.
Fig. 6 in The effect of β-cyclocitral treatment on the carotenoid content of transgenic Marsh grapefruit (Citrus paradisi Macf.) suspension-cultured cells
Fig. 6. Changes in metabolite pools of suspension-cultured cells resulting from fourteen days β-cyclocitral (0.5 mM) treatment. Asterisk indicate significance of difference at *P value <0.05, **P <0.01 and ***P <0.001, respectively. Red coloured asterisks indicate the relative metabolite contents increased by β-cc treatment whilst green represent a decrease. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
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.