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1,853 results for “cell culture”
Untargeted metabolomics analysis of RPE cells during six month in culture
<p>Primary RPE cell cultures were established with human fetal RPE cells acquired from ScienCell (Cat. No, 6540) seeded at passage 3 (P3) in 12-well Transwell<sup>®</sup> inserts (Corning Inc., Cat. No. CLSS3460) coated with 2% v/v Geltrex<sup>®</sup> matrix (Thermo Fisher Scientific; Cat. No. A1413202). Cells were cultured for a total time of 6 months (25 weeks), following the same protocol as previous works (16,59). Samples were acquired for protein immunolocalization, transcriptomic and metabolomics analysis from independent cell cultures along the total 6 months culture time (specifically at 4, 12, 17 and 25 weeks in culture), collecting 3 biological replicates per type of analysis and time point.<em> </em>Cell metabolites were quenched and extracted using MeOH:H<sub>2</sub>O (80:20, -20ºC) containing a spiked solution of isotopically enriched low molecular mass internal standard<strong>. </strong>Quality control (QC) samples were prepared by creating a pool of equal volumes from each biological replicate and were analyzed after a blank solution every fifth sample to monitor the performance, stability, and reproducibility of the LC-MS run. A liquid chromatography (LC) system 1290 Infinity II (Agilent Technologies) was coupled to an Agilent 6560B Ion Mobility quadrupole-time-of-flight mass spectrometer (IM-QTOF-MS) equipped with an Agilent G1607A dual jetstream ESI source and the MassHunter WorkSation 11.0. A reference solution containing purine and hexakis(1H,1H,3H-tetrafluoropropoxy)phosphazene for mass correction was added using the second ESI source. Chromatographic, ion source and MS conditions were optimized using QCs and selected parameters are shown in Supporting Information. MS analysis was conducted with an untargeted approach, operating the instrument in both positive and negative ionization modes. All samples were analysed in a randomized order. Raw data was processed using the software Profinder B10.00 (Agilent) and refined data were exported as CEF files<strong>. </strong>Data were converted to mzml files using MS convert.</p>
Zellige example dataset: primary culture of human bronchial cells infected by SARS-CoV-2
<p>A human bronchial epithelium was infected by SARS-CoV-2. The specimen was imaged four days post-infection. The z-stack image encompasses the very irregular epithelium surface. It was acquired with a point scanning microscope (Zeiss LSM700) equipped with Zeiss Plan-Apochromat 63x lens (NA=1.4). Pixel size 0.110µm, z step 0.4µm. This dataset contains both the ground-truth height map and the height map generated with Zellige. The Zellige parameters used are: <span class="math-tex">\(T_{A}=23, T_{otsu}=16, S_{min}=5, \sigma_{xy}=4, \sigma_{z}=1, T_{OSE1}=0.9, R_{1}=5, C_{1}=0.9, T_{OSE2}=0.1, R_{2}=5, C_{2}=0.8.\)</span>.</p> <p>Nota: to compare the ground truth height map with the Zellige height map, one first needs to substrat 1 to all values of the Zellige height map.</p> <p>See the related paper:<br> <a href="https://hal-pasteur.archives-ouvertes.fr/pasteur-03319522">https://hal-pasteur.archives-ouvertes.fr/pasteur-03319522</a></p> <p>See the accompanying paper: Extracting multiple surfaces from 3D microscopy images in complex biological tissues with the Zellige software tool. Trébeau <em>et al.</em> 2022: <a href="https://doi.org/10.1101/2022.04.05.485876">https://doi.org/10.1101/2022.04.05.485876</a></p> <p> </p>
DATA: Diversity of extracellular vesicles derived from calli, cell culture and apoplastic fluid of tobacco
<p><span>The data includes .jpg files with fluorescence readings and .csv files with results of concentration and size measurements.</span></p>
Full summary statistics of mixQTL for GTEx v8 Cells_Cultured_fibroblasts
The mixQTL method is described in paper doi.org/10.1101/2020.04.22.050666. Please cite the original paper if using the data.
Underlying and Extended Data for Refined and benchmarked homemade media for cost-effective, weekend-free human pluripotent stem cell culture
<p>Extended Data and raw data for the manuscript "Refined home-brew media for cost-effective, weekend-free hiPSC culture and genetic engineering"</p> <p> </p> <p dir="ltr">Extended Data 1.zip - protocol for preparation of the supplement for hE8 and B8+ media</p> <p dir="ltr">Extended Data 2.zip - Gene counts, supporting files, and output results of bulk analyses</p> <p dir="ltr">Extended Data 3.zip - Images of iPS cells adapted to cE8, hE8 and B8+ taken 24, 48 and 72 hours after passage. Contains raw .tiff files for each image and a .pdf with a compiled figure</p> <p dir="ltr">Extended Data 4.zip - Results of miloR analysis on the differences in the distribution of cells adapted to cE8, hE8 and B8+ to assigned monocle clusters </p> <p dir="ltr">Manuscript Data.zip – Raw data underlying the Figures 1, 2, 4, 5, 6 and 7.</p> <p>Bulk_RNA_seq_archive – archived source code used for generating results in Figure 3</p>
Raw Data for the article: Changes in the Transcriptome Profiles of Human Amnion-Derived Mesenchymal Stromal/Stem Cells Induced by Three-Dimensional Culture: A Potential Priming Strategy to Improve Their Properties
<p>Mesenchymal stromal/stem cells (MSCs) are believed to function in vivo as a homeostatic tool that shows therapeutic properties for tissue repair/regeneration. Conventionally, these cells are expanded in two-dimensional (2D) cultures, and, in that case, MSCs undergo genotypic/phenotypic changes resulting in a loss of their therapeutic capabilities. Moreover, several clinical trials using MSCs have shown controversial results with moderate/insufficient therapeutic responses. Different priming methods were tested to improve MSC effects, and three-dimensional (3D) culturing techniques were also examined. MSC spheroids display increased therapeutic properties, and, in this context, it is crucial to understand molecular changes underlying spheroid generation. To address these limitations, we performed RNA-seq on human amnion-derived MSCs (hAMSCs) cultured in both 2D and 3D conditions and examined the transcriptome changes associated with hAMSC spheroid formation. We found a large number of 3D culture-sensitive genes and identified selected genes related to 3D hAMSC therapeutic effects. In particular, we observed that these genes can regulate proliferation/differentiation, as well as immunomodulatory and angiogenic processes. We validated RNA-seq results by qRT-PCR and methylome analysis and investigation of secreted factors. Overall, our results showed that hAMSC spheroid culture represents a promising approach to cell-based therapy that could significantly impact hAMSC application in the field of regenerative medicine.</p>
Correlative microscopy of rat cultured hippocampal pyramidal cell from 40x confocal imaging to super-resolution 93x 3D STED of dendritic spines
<p>This dataset contain multi-scale image of rat hippocampal pyramidal cell related to our paper "<em>From tissues to segmentation: a modular framework for multi-scale neuron isolation</em>" by Cauzzo et al. <strong>Nature Comm (2024).</strong></p>
Colony Formation Dataset of Simulated Cell Cultures
<p>This is a dataset of synthetic cell colony formation generated by an off-lattice individual-based model. The calculated shape features of the artificial cell aggregates can be related to the parameter values of the simulated agents.</p>
FIG. 3 in The Bacterial Diversity Lurking in Protist Cell Cultures
FIG. 3. Relative abundance of each bacterial scaffold in Illumina sequencing libraries, represented as proportion of length normalized read pairs for the portion of each sequencing library mapping to the bacterial scaffolds. The two Alcanivorax sp. DSM 26293 scaffolds are marked with asterisks (*).
Germinal Center and Cultured B cell expression libraries
<p>Comparison of gene expression profiles between in vitro mitogen-activated spleen B lymphocytes and FACS-sorted Germinal Center B lymphocytes isolated from intestinal PeyerPatches of C57BL/6 mice. In order to explore gene expression signatures that may be orchestrating somatic hypermutation (SHM, also known as affinity maturation) during antigen-induced B lymphocyte differentiation in Germinal Centers (GC), we profiled whole transcriptome gene expression of ex vivo, commensal microflora-activated GC B-cells that exhibit efficient SHM, with in vitro activated B-cell blasts, which fail to undergo SHM. In In particular, we examine our hypothesis that differential expression or the DNA endonucleases apex1 and apex2 regulate SHM. Using Templated Oligo Sequencing (TempO-Seq®) in conjunction with conventional intracellular FACS staining and B lymphocyte cell sorting, we compare gene expression profiles of in vitro mitogen-activated (LPS and anti-IgD-dextran), short-term (48h) cultured B cell blasts with Germinal Center B-cells isolated from intestinal Peyer Patches (PP, identified by surface staining B220+, CD95+, GL7+), compared to each other and to naive PP B-cells (B220+, CD95-, GL7-). We find that unique, distinct transcriptional signatures dominate the DNA repair processes in GC B-cells or in vitro B-cell blast, shedding light on genomic processes that orchestrate efficient affinity maturation of B-cells during GC differentiation. We use Templated Oligo Sequencing (TempO-Seq), a RNA motif-specific short tandem Oligo DNA hybridization technique to quantitatively measure whole transcriptome mRNA in conjunction with conventional surface membrane, fixable live/dead discriminator dye, and intracytoplasmic fluorescence antibody staining followed by FACS to isolate B cell populations of interest.</p>
Synthesis of large scale 3D microscopic images of 3D cell cultures for training and benchmarking
<p>Accompaning data to the paper:</p> <p>Synthesis of large scale 3D microscopic images of 3D cell cultures for training and benchmarking</p>
Confocal microscopy images (CZI files) of human chondrocytes in different cell culture media with stained nuclei and primary cilia
<p>1. Methods</p> <p>1.1 Cell culture</p> <p>For investigating the influence of the cell culture medium composition on the lengths of primary cilia, human non-degenerative chondrocytes from a 30-year-old male donor (NHAC-kn, CC-2550; LONZA, Walkersville Inc., Walkersville, MD, USA) were used. These chondrocytes were seeded in passage four with a density of 28000 cells/cm<sup>2</sup> on collagen-coated glass coverslips (GG-15-Collagen; Neuvitro Corporation, Camas, WA, USA). The cells were cultivated in 12-well plates (Thermo Fisher Scientific Inc., Waltham, MA, USA) under hypoxic conditions at 37°C, 5% CO<sub>2</sub> and 5% O<sub>2</sub> with different media compositions for three days.<br> The basal medium consisted of Dulbecco’s Modified Eagle Medium (DMEM) (Gibco™) including high glucose (GlutaMAX™), sodium pyruvate supplements (Thermo Fisher Scientific Inc., Waltham, MA, USA), as well as 1% penicillin/streptomycin (Pen/Strep; Thermo Fisher Scientific Inc.), 1% Amphotericin B (Biochrom GmbH, Berlin, Germany), and 50 µg mL<sup>−1</sup> ascorbic acid (Sigma-Aldrich, Merck KGaA, Darmstadt, Germany). To this basal medium, different supplements were added, creating four groups:<br> 1) ITS: 1% Insulin-Transferrin-Selenium (ITS+™ Premix, BD Biosciences, Franklin Lakes, NJ, USA),<br> 2) ITS with Dexa: 1% Insulin-Transferrin-Selenium (ITS+™) and 100 nM dexamethasone (Sigma-Aldrich, Merck KGaA, Darmstadt, Germany),<br> 3) ITS with Dexa + IGF-1 + TGF-β1: 1% Insulin-Transferrin-Selenium (ITS+™), 100 nM dexamethasone, 50 ng mL<sup>−1</sup> insulin-like growth factor (IGF)-1 (R&D Systems, Minneapolis, MN, USA) and 50 ng mL<sup>−1</sup> transforming growth factor (TGF)-β1 (Peprotec, Hamburg, Germany),<br> 4) FBS: 10% fetal bovine serum (FBS, Pan Biotech, Aidenbach, Germany).</p> <p>1.2 Immunocytochemistry</p> <p>After three days of cultivation in the different media compositions, the chondrocytes were washed once with phosphate-buffered saline (PBS; Biochrom GmbH, Berlin, Germany) and fixed for 10 min at room temperature (RT) with 4% paraformaldehyde (ROTI ® Histofix, Carl Roth GmbH + Co. KG, Karlsruhe, Germany). After fixation, cells were washed again and permeabilized with 0.2% Triton-X100 (Merck, Darmstadt, Germany) for 10 min. For blocking the unspecific binding sites, cell-seeded coverslips were incubated with bovine serum albumin (BSA; Sigma-Aldrich) with a concentration of 5% in PBS for one hour at RT after another washing step with PBS. To stain the primary cilium, cells were incubated with anti-acetylated α-tubulin (6-11B-1) (RRID: AB 628409) labeled with Alexa Fluor 647 (sc-23950 AF647, Santa Cruz Biotechnology, Dallas, TX, USA) diluted 1:200 in PBS at 4°C overnight. Additionally, the Actin cytoskeleton was stained with Acti-stain 488 Fluorescent Phalloidin (Cytoskeleton, Inc., Denver, CO, USA) diluted 10 in PBS for 30 min at RT. Afterward, cells were washed three times with PBS, and the coverslips were fixed with Fluoroshield™ (Sigma-Aldrich) containing 4’,6-Diamidino-2-phenylindole (DAPI).</p> <p>1.3 Image acquisition</p> <p>Three-dimensional fluorescence images of stained cells were acquired with a ZEISS ELYRA LSM 780 confocal laser scanning microscope (CLSM) (Carl Zeiss AG, Oberkochen, Germany). Images were recorded using a Plan-Apochromat 63×/1.40 Oil DIC M27 objective (Carl Zeiss AG, Oberkochen, Germany). The distance of two layers was 0.2814 µm and the resolution 1024 × 1024 pixels (scan magnification: 0.6, pixel length: 0.2196 µm).</p>
Whole-cell Escherichia coli lactate biosensor for monitoring mammalian cell cultures during biopharmaceutical production-- dataset
<p>Raw data for Goers et al, (2017), Biotech Bioeng. doi:10.1002/bit.26254.</p> <p>Each graph including the supplementary figures is a separate tab.</p>
Targeted DNA-seq analysis was performed on sorted population of CD45+/CD34+ HSPCs from control or FLI-1 modified mRNA treated mPB after co-culture with vascular niche cells
<p>Human mPB HSPCs were harvested isolated and transduced with either control or FLI-1 modified mRNA. HSPCs were introduced into co-culture with vascular niche ECs. Cultures were harvested and CD45+/CD34+ HSPCs were resoerted and processed for trageted DNA-seq analysis. Contains raw FASTQ sequencing files, unfiltered VCFs, and curated results in an excel.</p>
A gas-only bioreactor system maintains stable culture environments and reveals that moderate pH deviations trigger transcriptome-wide responses in human cells cultured in physioxia and physiological buffers
<p><span>Although pH instability is emerging as a potential driver of changes in cell physiology, pH is still poorly controlled during cell culture and in vitro experiments. Standard procedures include the use of chemicals usually not present in the primary physiological buffering system (CO<sub>2</sub>/HCO<sub>3</sub><sup>-</sup>), such as acids and bases, to manipulate pH levels. This, however, leads to artifacts that potentially affect scientists' findings. </span><span>Here, we propose a novel method for controlling pH levels by relying only on the physiological buffering system. pH was manipulated in a repurposed commercial bioreactor set-up, using a two-sided control loop of CO<sub>2</sub> and N<sub>2</sub> gas in NaHCO<sub>3</sub>--buffered medium. This method produces optimal and stable dO<sub>2</sub> </span><span>profiles and tightly maintains pH levels. With this procedure, we analyzed the effects of different pH levels (6.8, 7.0, 7.2, and 7.4) on the performance and transcriptome of the human GM12878 cell line over a 72-hours experiment. Our results showed that inflammation and negative cellular proliferation are among the signatures activated at low pH. This further highlights the importance of a thorough pH control during cell culture. </span></p>
THP-1 DNase I cell culture under confocal microscope
<p>THP-1 DNase I cell imaged in suspension using a confocal microscope LSM780 Zeiss</p> <p>The cells have their nucleus, membrane, and mitochondria stained respectively using DAPI, Phalloidin, and TOMM20.</p> <p>The mitochondria signal is deconvoluted using Huygens SVI software.</p> <p>This is a high magnification cell culture data example for cell segmentation and mitochondria segmentation in 3D.</p> <p> </p>
Remotely controlled 3D-engineered scaffolds for biomimetic in vitro investigations on brain cell co-cultures
Open the record for dataset details and reuse information.
Closed loop recordings from IPSC cell culture using planar MEA
<p>Recordings from IPSC cell culture using planar MEA in closed loop with the AlzModel. </p> <p>The script 'alzgraphs.py' is used to display summary statistics. </p>
Figure 6 in Potential neuroprotective of trans-resveratrol a promising agent tempeh and soybean seed coats-derived against beta-amyloid neurotoxicity on primary culture of nerve cells induced by 2-methoxyethanol
Figure 6. Treatment Group with resveratrol standard after induced by Beta-Amyloid (10 x10).
Figure 3 in Potential neuroprotective of trans-resveratrol a promising agent tempeh and soybean seed coats-derived against beta-amyloid neurotoxicity on primary culture of nerve cells induced by 2-methoxyethanol
Figure 3. Treatment group: 2- ME + Resveratrol isolated from Tempeh (10 x10).
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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.