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Cells

Cells are the fundamental units of life, the building blocks of all living organisms.
They come in a vast array of shapes, sizes, and specializations, from the simplest single-celled bacteria to the highly complex human cells.
Understanding the intricate workings of cells is crucial for advancineg medical research and developing new treatments.
PubCompare.ai's AI-driven platform helps researchers optimize their cell research by locating the best protocols from literature, pre-prints, and patents.
Its unique comparison tools use advanced AI to enhance reproducibility and accuracy, ensuring your cell experiments yield reliable results.
Experiance the power of PubCompare.ai today and unlock new insights into the mysterious world of cells.

Most cited protocols related to «Cells»

Aside from the highly popular SCLVM (https://github.com/PMBio/scLVM) [46 (link), 47 (link)], which uses Gaussian process latent variable models for inferring hidden sources of variation, there are, among others, the visualization frameworks FASTPROJECT (https://github.com/YosefLab/FastProject) [48 (link)], ACCENSE (http://www.cellaccense.com/) [49 ], and SPRING (https://github.com/AllonKleinLab/SPRING) [15 ]—the latter uses the JavaScript package (http://d3js.org D3.js for the actual visualization and Python only for preprocessing—the trajectory inference tool SCIMITAR (https://github.com/dimenwarper/scimitar), the clustering tool PHENOGRAPH (https://github.com/jacoblevine/PhenoGraph) [19 (link)], the single-cell experiment design tool MIMOSCA (https://github.com/asncd/MIMOSCA)[50 (link)], UMIS (https://github.com/vals/umis) for handling raw read data [51 (link)], the tree-inference tool ECLAIR (https://github.com/GGiecold/ECLAIR) [52 (link)], and the framework FLOTILLA (https://github.com/yeolab/flotilla), which comes with modules for simple visualization, simple clustering, and differential expression testing. Hence, only the latter provides a data analysis framework that solves more than one specific task. In contrast to SCANPY, however, FLOTILLA is neither targeted at single-cell nor at large-scale data and does not provide any graph-based methods, which are the core of SCANPY. Also, FLOTILLA is built around a complicated class STUDY, which contains data, tools, and plotting functions. SCANPY, by contrast, is built around a simple HDF5-backed class ANNDATA, which makes SCANPY both scalable and extendable (law of Demeter).
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Publication 2018
Cells Python Trees Vals

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Publication 2019
Cells Chromium Gene Expression Genes Genes, vif Germ Cells Homo sapiens Human Body Mitochondrial Inheritance PBMC Peripheral Blood Mononuclear Cells Single-Cell RNA-Seq XCL1 protein, human
We obtained a read count matrix for the SMART-Seq2 dataset (Nestorawa et al.)37 under the GEO accession GSE81682, and considered 765 annotated progenitors cells expressing at least 4,000 genes. The authors generously provided lineage annotations for each cell (corresponding to Figure 4 in the original publication, used in our Figure 3). We obtained a batch-corrected UMI count matrix for the MARS-Seq dataset38 (link) from the authors’ online resource (http://compgenomics.weizmann.ac.il/tanay/?page_id=649), where we also obtained the MARS-Seq cluster IDs for each cell. This dataset had been previously filtered to remove cells with less than 500 detected UMI for a total of 2,686 single cells.
Both datasets contain cycling progenitors, and heterogeneity between cell cycle stages for these cells has been previously been shown to confound developmental analyses. Therefore, independently for both datasets, we first assigned a cell cycle score to each cell using the PCA method57 (link) on a previously annotated list of cell cycle genes58 (link). We then used the ScaleData function in Seurat (using the cell cycle score as latent variable in a linear regression framework) to mitigate this source of variation in the dataset, prior to CCA.
Publication 2018
Cells Genes Genetic Heterogeneity Stem Cells
Nuclear RNA was prepared from HEK293T (kidney) cells. Briefly, cells were lysed on ice for 5 min in 10 mM Tris-HCl pH 7.5, 10 mM NaCl, 0.2 mM EDTA, 0.05% NP-40, and nuclei were spun at 2,500g for 3 min and then resuspended in QIAzol for RNA isolation using the miRNeasy kit according to the manufacturer’s instructions (Qiagen). The RNA-seq library was created using the Illumina TruSeq RNA Sample Preparation Kit v2 with the standard protocol, and sequenced on one lane of the HiSeq 2000 platform (100 bp, paired-end). Data are available at NCBI as accession number SRP041943. The database of annotated protein coding and noncoding genes (41,409 genes and 171,904 transcripts in total) was produced by merging all annotated genes from the RefSeq database29 (link), the UCSC Browser24 (link) and the Ensembl database30 (link).
Publication 2015
Cell Nucleus Cells DNA Library Edetic Acid Genes isolation Kidney Nonidet P-40 RNA, Nuclear RNA-Seq Sodium Chloride Standard Preparations Tromethamine
Large-scale, arrayed format RNAi screens to identify genes essential for proliferation/viability were performed as described3 (link),14 (link). The effect of introducing each of the 5002 shRNAs (targeting 957 genes) was determined in 19 cell lines, and normalized using the B-score metric4 (link). Feature selection of shRNA B-score data was performed using the Comparative Marker Application Suite in GenePattern5 (link) and was independently analyzed using RIGER analysis6 (link) to compute NES for each gene. Secondary screen viability data was normalized using a percent of control statistic, given the biased nature of the candidate shRNA plate. Expression profiling was used to generate a signature that correlates with KRAS activation and implicated NF-κB signaling in cell lines and tumors dependent on KRAS. Regulation of NF-κB by TBK1 was shown using biochemical and cell biological approaches. Details of the analytical methods are provided in the Full Methods.
Publication 2009
Biopharmaceuticals Cell Lines Cells Genes K-ras Genes Neoplasms RELA protein, human RNA Interference Short Hairpin RNA TBK1 protein, human

Most recents protocols related to «Cells»

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Example 5

MTT cytotoxicity assays were used to assess the cytotoxicity of RGQDs/Nd-GQDs/Tm-GQDs. HeLa cells were plated in a 96-well plate with 5000 cells per well (100 μL/well) and kept in an incubator overnight at 37.1° C. while maintaining the CO2/air ratio of 1:19. After 24 h of incubation, the samples were added into each well at different concentrations for different materials (0 to 70 μg/mL, 1 mg/ml, 0.25 mg/ml for RGQDs, Nd-GQDs, Tm-GQDs, respectively). After 24 h of incubation, the medium was replaced by 100 μL of 1 mg/mL thiazolyl blue tetrazolium bromide. After 4 h of further incubation, MTT (3-(4-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) was replaced with 100 μL of DMSO (dimethyl sulfoxide) to solubilize the precipitation. Reduction in MTT influences the metabolic activity of living cells, which can be assessed with absorbance measurements because living cells metabolize the MTT and form a highly absorbing purple colored byproduct known as formazan. The absorbance (essentially the cell viability) of the final sample was measured at 540 nm wavelength using the FLUOstar Omega microplate reader.

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Patent 2024
Biological Assay Bromides Cells Cell Survival Cytotoxin Formazans HeLa Cells Sulfoxide, Dimethyl thiazolyl blue tetrazolium bromide

Example 14

The ability of anti-PD-L1 antibodies to modulate immune responsiveness was assessed using a mixed lymphocyte reaction (MLR). With this assay, the effects anti-PD-L1 antibodies on cell activation and the production of IL-2 were measured. The MLR was performed by culturing 105 purified human CD4+ cells from one donor with 104 monocyte derived dendritic cells prepared from another donor. To prepare the dendritic cells, purified monocytes were cultured with GM-CSF (1,000 U/ml) and IL-4 (500 U/ml) for seven days. Anti-PD-L1 or control antibodies were added to the allogeneic MLR cultures at 10 μg/ml unless stated otherwise. Parallel plates were set up to allow collection of supernatants at day 3 and at day 5 to measure IL-2 using a commercial ELISA kit (Biolegend). The antibodies used were the disclosed H6B1L, RSA1, RA3, RC5, SH1E2, SH1E4, SH1B11, and SH1C8 as compared to prior disclosed antibodies 10A5 (Bristol-Myers-Squibb/Medarex) and YW243.55S70 (Roche/Genentech) that were obtained via in-house production from prior-disclosed antibody sequences (U.S. Patent Application 2009/0055944 and U.S. Patent Application US 2010/0203056; the disclosure of which are incorporated by reference herein).

Production of IL-2 was enhanced by the addition of the anti-PD-L1 antibodies.

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Patent 2024
Anti-Antibodies Antibodies Antigens Binding Proteins Biological Assay CD274 protein, human Cells Dendritic Cells Enzyme-Linked Immunosorbent Assay Granulocyte-Macrophage Colony-Stimulating Factor Homo sapiens Immunoglobulins Lymphocyte Culture Test, Mixed Monocytes Tissue Donors

Example 3

Human primary sebocytes (Zenbio, RTP, NC) were plated at confluence on 96 well Scintiplates and allowed to adhere overnight. Cells were treated with the SCD1 inhibitor Compound A prepared in media containing the LXR agonist and insulin and cultured overnight. The DGAT inhibitor A922500 (2 μM) was included as a positive control. The following day 14C-acetate was added to each well and the plate was gently mixed. Cells were placed in the incubator at 37° C. for 4 hours total. After 2 hours of incubation the Cell Titer Blue (CTB) assay was started, 10 μl of CTB reagent was added to each well and incubated for the remaining 2 hours at 37° C. Following the 4 hour incubation, the RFU was determined using the SpectraMax Gemini EM under the following parameters: 560ex/590em with a 570 cutoff, top read. The medium was removed and cells were washed 3× with PBS. All of the PBS was removed from the wells and the plates were allowed to air dry. The plate was read in the MicroBeta TriLux counter and data was analyzed as CPM and normalized to CTB readout. Data is shown in FIG. 2.

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Patent 2024
Acetate Biological Assay Cells Homo sapiens Insulin N,N,N-triethyl-11-(4-methyl-2-oxo-2H-chromen-7-yloxy)-11-oxoundecan-1-aminium bromide Psychological Inhibition

Example 3

Reactivity of the antibodies of the invention against several species of mesothelin (cyno, rat, mouse) was tested using assays well known in the art. The data is summarized in FIG. 4.

FACS binding assays were performed to evaluate the binding of the anti-Mesothlelin antibodies to murine, rat and cynomologous monkey mesothelin orthologues, using recombinant forms of the various receptors transiently expressed on 293T cells. FACs assays were performed by incubating hybridoma supernatants with 10,000 to 25,000 cells in PBS/2% Fetal bovine serum/2 mM Calcium Chloride at 4° C. for one hour followed by two washes with PBS/2% Fetal bovine serum/2 mM Calcium Chloride. Cells were then treated with florochrome-labeled secondary antibodies at 4° C. followed by one wash. The cells were resuspended in 50 μl of PBS/2% FBS and antibody binding was analyzed using a FACSCalibur™ instrument.

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Patent 2024
Anti-Antibodies Antibodies Biological Assay Calcium chloride Cells Cross Reactions HEK293 Cells Hybridomas Immunoglobulins Mesothelin Monkeys Mus
Not available on PMC !

Example 10

This example provides in vitro IC50 data for the blocking of the interaction between recombinant human PD-1 (PD-1-Fc Chimera; Sino Biologics) and human PD-L1 expressed CHO cells by anti-PD-L1 antibody G12. Here, CHO cells expressing PD-L1 were pre-incubated with G12 prior to the addition of rhPD-1-Fc chimeric protein. After incubation and washing, PD-1 binding to cell surface expressed PD-L1 was detected using an Alexa-Fluor 647 tagged anti-PD-1 antibody by flow cytometry (Intellicyt HTFC; FL-4H). This example shows that anti-PD-L1 monoclonal antibody G12 was able to inhibit efficiently the binding of PD-1 to PD-L1 expressed on the surface of CHO cells.

Results: As shown in FIG. 8 and Table 4, the IC50 for blocking of the PD-1/PD-L1 cellular interaction by G12 is 1.76E-09 M. Data was collected on the Intellicyt HTFC flow cytometer, processed using FlowJo software, and analyzed and plotted in Graph Pad Prizm using non-linear regression fit. Data points are shown as the median fluorescence detected in the FL-4H channel+/−Std Error.

TABLE 4
G12
Inhibition of PD-1/PD-L1CHO-PD-L1/1.76E−09
Interaction IC50 (M)rhPD-1-Fc

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Patent 2024
Alexa Fluor 647 Antibodies, Anti-Idiotypic Antigens Binding Proteins Biological Factors CD274 protein, human Cell Communication Cells Chimera CHO Cells Flow Cytometry Fluorescence Homo sapiens Immunoglobulins isononanoyl oxybenzene sulfonate Monoclonal Antibodies Proteins Psychological Inhibition

Top products related to «Cells»

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Fetal Bovine Serum (FBS) is a cell culture supplement derived from the blood of bovine fetuses. FBS provides a source of proteins, growth factors, and other components that support the growth and maintenance of various cell types in in vitro cell culture applications.
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Lipofectamine 2000 is a cationic lipid-based transfection reagent designed for efficient and reliable delivery of nucleic acids, such as plasmid DNA and small interfering RNA (siRNA), into a wide range of eukaryotic cell types. It facilitates the formation of complexes between the nucleic acid and the lipid components, which can then be introduced into cells to enable gene expression or gene silencing studies.
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DMEM (Dulbecco's Modified Eagle's Medium) is a cell culture medium formulated to support the growth and maintenance of a variety of cell types, including mammalian cells. It provides essential nutrients, amino acids, vitamins, and other components necessary for cell proliferation and survival in an in vitro environment.
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Penicillin/streptomycin is a commonly used antibiotic solution for cell culture applications. It contains a combination of penicillin and streptomycin, which are broad-spectrum antibiotics that inhibit the growth of both Gram-positive and Gram-negative bacteria.
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TRIzol reagent is a monophasic solution of phenol, guanidine isothiocyanate, and other proprietary components designed for the isolation of total RNA, DNA, and proteins from a variety of biological samples. The reagent maintains the integrity of the RNA while disrupting cells and dissolving cell components.
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Penicillin is a type of antibiotic used in laboratory settings. It is a broad-spectrum antimicrobial agent effective against a variety of bacteria. Penicillin functions by disrupting the bacterial cell wall, leading to cell death.
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Streptomycin is a broad-spectrum antibiotic used in laboratory settings. It functions as a protein synthesis inhibitor, targeting the 30S subunit of bacterial ribosomes, which plays a crucial role in the translation of genetic information into proteins. Streptomycin is commonly used in microbiological research and applications that require selective inhibition of bacterial growth.
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The FACSCalibur is a flow cytometry system designed for multi-parameter analysis of cells and other particles. It features a blue (488 nm) and a red (635 nm) laser for excitation of fluorescent dyes. The instrument is capable of detecting forward scatter, side scatter, and up to four fluorescent parameters simultaneously.
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Lipofectamine 3000 is a transfection reagent used for the efficient delivery of nucleic acids, such as plasmid DNA, siRNA, and mRNA, into a variety of mammalian cell types. It facilitates the entry of these molecules into the cells, enabling their expression or silencing.
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RPMI 1640 medium is a commonly used cell culture medium developed at Roswell Park Memorial Institute. It is a balanced salt solution that provides essential nutrients, vitamins, and amino acids to support the growth and maintenance of a variety of cell types in vitro.

More about "Cells"

Cells are the fundamental building blocks of all living organisms, from the simplest single-celled bacteria to the highly complex human cells.
These microscopic structures come in a vast array of shapes, sizes, and specializations, each playing a crucial role in the intricate workings of life.
Understanding the complexities of cellular biology is essential for advancing medical research and developing new treatments.
At the heart of cell research lies a diverse array of laboratory techniques and tools.
Fetal bovine serum (FBS) is a commonly used supplement in cell culture media, providing essential nutrients and growth factors for cell proliferation.
Lipofectamine 2000 and Lipofectamine 3000 are transfection reagents that facilitate the introduction of genetic materials into cells, allowing researchers to study gene expression and function.
Commonly used cell culture media include DMEM (Dulbecco's Modified Eagle Medium) and RPMI 1640, which provide the necessary nutrients and environment for cells to thrive.
Antibiotics such as Penicillin and Streptomycin are often added to these media to prevent bacterial contamination, ensuring the integrity of cell cultures.
For analyzing cellular characteristics and behavior, researchers rely on advanced instruments like the FACSCalibur flow cytometer.
This powerful tool enables the precise quantification and sorting of individual cells based on their physical and fluorescent properties.
When it comes to extracting and analyzing cellular biomolecules, reagents like TRIzol play a crucial role.
TRIzol is a popular solution used for the isolation of high-quality RNA, DNA, and proteins from cells, facilitating downstream analyses and investigations.
PubCompare.ai's AI-driven platform harnesses the power of these essential tools and techniques, helping researchers optimize their cell research by locating the best protocols from literature, pre-prints, and patents.
Its unique comparison tools use advanced artificial intelligence to enhance reproducibility and accuracy, ensuring that your cell experiments yield reliable and insightful results.
Experience the power of PubCompare.ai today and unlock new discoveries in the mysterious world of cells.