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G2 Phase

Q: What are some common challenges researchers face when studying the G2 phase?

One of the key challenges in G2 phase research is identifying the most effective and reproducible protocols from the vast amount of scientific literature, pre-prints, and patents. Researchers may struggle to pinpoint the optimal protocols that are tailored to their specific research goals and experimental conditions.

The G2 phase is a critical stage in the cell cycle, occurring between the S phase and the M phase.
During this phase, the cell prepares for mitosis by synthesizing the necessary proteins and organelles.
The G2 phase is characterized by increased metabolic activity, DNA repair, and the assembly of the mitotic spindle.
Optimizing G2 phase research is crucial for understanding cell division, development, and disease processes.
PubCompare.ai, an AI-driven platform, can help researchers find the best scientific protocols from the literature, pre-prints, and patents, saving time and effort in identifying the most reproducible and accurate protocols for their G2 phase research needs.

Most cited protocols related to «G2 Phase»

Profiling Mitochondrial Dynamics Using FACS-Based BH3 Assay

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Publication 2013

B-Lymphocytes Biological Assay Carbonyl Cyanide p-Trifluoromethoxyphenylhydrazone Cells Discrimination, Psychology Fluorescence G2 Phase Genetic Heterogeneity Mitochondria Mitochondrial Inheritance Peptides Population Group Rhodamine 123 Stains Sulfoxide, Dimethyl Tissues

Revealing Cell Cycle Dynamics in Single Cells

Analysis of single-cell RNA-seq in human (293T) and mouse (3T3) cell lines^{20 (link)}, and in mouse haematopoietic stem cells^{21 (link)} revealed in each case two prominent cell cycle expression programs that overlap considerably with genes that are known to function in replication and mitosis, respectively, and that have also been found to be expressed at G1/S phases and G2/M phases, respectively, in bulk samples of synchronized HeLa cells^{33 (link)}. We thus defined a core set of 43 G1/S and 55 G2/M genes that included those genes that were detected in the corresponding expression clusters in all four datasets from the three studies described above (Supplementary Table 2). As expected, the genes in each of those expression programs were highly co-regulated in a small fraction of the oligodendroglioma cells, such that some cells expressed only the G1/S or the G2/M programs and other cells expressed both programs (Extended Data Fig. 6a). Plotting the average expression of these programs revealed an approximate circle (Fig. 3a), which we hypothesize describes the progression along the cell cycle. Putative cycling cells were identified by at least a twofold upregulation and a t-test P value < 0.01 for either the G1/S or the G2/M gene set compared to the average of all cells. Although we cannot confidently define the regions that correspond to each phase of the cell cycle in an automatic way, we manually defined four regions in the apparent circle and assigned them to approximate cell cycle phases.

Tirosh I., Venteicher A.S., Hebert C., Escalante L.E., Patel A.P., Yizhak K., Fisher J.M., Rodman C., Mount C., Filbin M.G., Neftel C., Desai N., Nyman J., Izar B., Luo C.C., Francis J.M., Patel A.A., Onozato M.L., Riggi N., Livak K.J., Gennert D., Satija R., Nahed B.V., Curry W.T., Martuza R.L., Mylvaganam R., Iafrate A.J., Frosch M.P., Golub T.R., Rivera M.N., Getz G., Rozenblatt-Rosen O., Cahill D.P., Monje M., Bernstein B.E., Louis D.N., Regev A, & Suvà M.L. (2016). Single-cell RNA-seq supports a developmental hierarchy in human oligodendroglioma. Nature, 539(7628), 309-313.

Publication 2016

3T3 Cells Cell Cycle Cells Dietary Fiber Disease Progression DNA Replication G2 Phase Gene Expression Genes HeLa Cells Hematopoietic System Homo sapiens Mitosis Mus Oligodendroglioma Single-Cell RNA-Seq Stem, Plant Transcriptional Activation

Functional Enrichment Analysis of Fission Yeast Genes

All analyses for functional enrichments were performed using a set of GO lists based on fission and budding yeast GOslim annotations (release September 2011). This set was complemented with a series of lists based on gene expression. Five lists of cell-cycle regulated genes were derived from (Rustici et al., 2004 (link)) and contain either all periodic genes, or periodic genes peaking in G1, S, M, or G2 phases of the cell cycle. Two lists contained genes of the core environmental stress response (CESR), either induced (”stress-related”) or repressed (”growth-related”) during stress (Chen et al., 2003 (link)). Four lists contained genes regulated upon nitrogen removal or during early, middle, or late meiosis (Mata et al., 2002 (link)). Finally 4 lists were computed in our laboratory and contained the 10% shortest and the 10% longest mRNAs, a list of transcription factors, and a list of proteins containing RNA-recognition (RRM) motifs (based on annotation available in PomBase) (Wood et al., 2012 (link)). Table S17 provides a list of the genes included in each functional category used in this study.
For the sliding-window analysis in Figure 2, all fission yeast mRNAs were ranked based on absolute expression. The level and significance of the overlap between a sliding window of 200 genes of increasing absolute expression levels and specific functional categories/gene lists were recorded. Significance of the overlaps was tested using a Fisher exact test, and p-values were corrected for multiple testing using the ‘FDR’ method.

Marguerat S., Schmidt A., Codlin S., Chen W., Aebersold R, & Bähler J. (2012). Quantitative Analysis of Fission Yeast Transcriptomes and Proteomes in Proliferating and Quiescent Cells. Cell, 151(3), 671-683.

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Publication 2012

Cell Cycle G2 Phase Gene Expression Genes Genes, cdc Genes, vif Meiosis Nitrogen RNA, Messenger Saccharomycetales Schizosaccharomyces pombe Staphylococcal Protein A Transcription Factor

Comparative Replication Timing Profiling

To generate replication timing profiles we calculated the ratio of uniquely mapped reads in the replicating (S phase) sample to the nonreplicating (G2 phase) sample. Custom Perl scripts (available on request) were used to independently calculate this ratio for every 1-kb window. We excluded windows where fewer than 250 reads were mapped in either sample. The resulting absolute ratios reflect the read numbers; therefore, we normalized data by dividing by an empirically determined factor. This resulted in >95% of the data points lying between 1 and 2 (a biologically imposed restraint). Resulting replication profiles were subjected to smoothing using a Fourier transformation, essentially as described previously (Raghuraman et al. 2001 (link)), but excluding regions close to chromosome ends and regions with low data density (e.g., nonunique repeat units).
To compare replication profiles between species we used the liftOver tool to project smoothed data from the genome assembly of one species to the S. cerevisiae genome. Pearson correlation coefficients were calculated for all pairwise species combinations, limiting comparisons to genomic positions where data are available from all four species. Intersections between data sets were performed using the program closestBed (from BEDtools). The difference in replication time between species was calculated by subtracting the relative copy number in one species by that from the other (at those points where data was available for both species as determined using liftOver). Differences in gene expression level (Tsankov et al. 2010 (link)) were calculated for 4547 genes for which data was available in both species.

Müller C.A, & Nieduszynski C.A. (2012). Conservation of replication timing reveals global and local regulation of replication origin activity. Genome Research, 22(10), 1953-1962.

Publication 2012

Chromosomes DNA Replication G2 Phase Gene Expression Genes Genome Intersectional Framework Saccharomyces cerevisiae

Cell Cycle Analysis of LSK and HSC

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Publication 2013

Antibodies Antibodies, Anti-Idiotypic Cells Division Phase, Cell Ethanol Fluorescein-5-isothiocyanate Fluorescent Dyes G2 Phase HOE 33342 Macrophage-1 Antigen Propidium Iodide Pyronine signaling lymphocytic activation molecule, human Spinocerebellar Ataxia Type 1 Stem Cells, Hematopoietic

Most recents protocols related to «G2 Phase»

Cell Cycle Analysis by Flow Cytometry

Cells were treated in three biological repeats for 72 h, collected using 0.25% trypsin in EDTA and washed twice in PBS. Cells were fixed in ice-cold 70% ethanol, washed in ice-cold PBS, and stained in 500 µL PI/Triton X-100 solution, containing 100 µg/mL DNAase-free RNAse A (Sigma Chemical Co.), 50 µg/mL propidium iodide (Sigma Chemical Co.), and 0.25% (v/v) Triton X-100 (Sigma Chemical Co.) in PBS, for 1.5 h at room temperature in dark. Cells are then washed in cold PBS and analyzed by a flow cytometer (BD Accuri C6, BD Biosciences, Franklin Lakes, NJ). Data from at least 10,000 events per sample were collected and presented as proportions of the cells in G0/G1, S, and G2/M phases using ModFit LT 5.0 software (Verity Software House, Topsham, ME). Experiments were repeated in three triplicates.

Chan L.S., Liu J., Li M.S., Li L., Tao Q, & Mok T.S. (2023). Selenite as a dual apoptotic and ferroptotic agent synergizes with EGFR and KRAS inhibitors with epigenetic interference. Clinical Epigenetics, 15, 36.

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Publication 2023

Biopharmaceuticals Cells Cold Temperature Deoxyribonucleases Edetic Acid Endoribonucleases Ethanol G2 Phase Propidium Iodide Triton X-100 Trypsin

Comparative Cell Cycle Analysis of Vasculogenic Clusters

To check the cycling difference between the vasculogenic cluster and parent cluster different clusters post miR-200b inhibition, cell cycle analyses were performed to identify the ratio of dividing cells and non-proliferating cells within clusters 0 and 1. Assigning cell cycle phase for each cell within clusters 0 and 1 was performed using the function CellCycleScoring in Seurat^{28 (link),65 (link)}. The canonical marker genes for S and G2/M phases as previously published were used to calculate cell cycle scores^{66 (link)}. Cells expressing markers for either S or G2/M phases were assigned to their corresponding phase (high proliferation score), while cells not expressing mitotic marker genes were assigned to G1 phase. Next, the number of cells in each cell cycle phase within clusters 0 and 1 was counted. There was no significant change was observed between the cells present in proliferation phase (G2M and S phase) between the clusters 0 and 1 (Ordinary two-way ANOVA test, p > 0.05).

Pal D., Ghatak S., Singh K., Abouhashem A.S., Kumar M., El Masry M.S., Mohanty S.K., Palakurti R., Rustagi Y., Tabasum S., Khona D.K., Khanna S., Kacar S., Srivastava R., Bhasme P., Verma S.S., Hernandez E., Sharma A., Reese D., Verma P., Ghosh N., Gorain M., Wan J., Liu S., Liu Y., Castro N.H., Gnyawali S.C., Lawrence W., Moore J., Perez D.G., Roy S., Yoder M.C, & Sen C.K. (2023). Identification of a physiologic vasculogenic fibroblast state to achieve tissue repair. Nature Communications, 14, 1129.

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Publication 2023

Cell Cycle Cells G1 Phase G2 Phase Genes Menstrual Cycle, Proliferative Phase neuro-oncological ventral antigen 2, human Parent Psychological Inhibition

Investigating [77Br]Br-WC-DZ's Impact on Prostate Cancer Cell Cycle

The effect of [⁷⁷Br]Br-WC-DZ in altering the cell cycle phases of prostate cancer cells PC-3 and IGR-CaP1 was analyzed using a Muse™ Cell Cycle Kit (Luminex, Austin, TX, USA) according to the manufacturer’s instructions. Briefly, after incubating the cells with [⁷⁷Br]Br-WC-DZ (1 nM and 5 nM) for 24 h, the cells were harvested using trypsin and washed with PBS. The cells were then fixed with 70% ethanol kept at −20 °C. The cells were then washed, pelleted, and incubated with Muse cell cycle reagent for 30 min at room temperature in the dark. The percentage of cells in G0/G1, S, and G2/M phases were assessed in Guava Muse™ Cell Analyzer (Luminex, Austin, TX, USA).

Sreekumar S., Zhou D., Mpoy C., Schenk E., Scott J., Arbeit J.M., Xu J, & Rogers B.E. (2023). Preclinical Efficacy of a PARP-1 Targeted Auger-Emitting Radionuclide in Prostate Cancer. International Journal of Molecular Sciences, 24(4), 3083.

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Publication 2023

austin Cell Cycle Cells Ethanol G2 Phase Muse PC 3 Cell Line Prostate Psidium guajava Staging, Cancer Trypsin

Xanthone Impact on HepG2 Cell Cycle

Human liver cancer cells HepG2 (1 × 10⁶) were cultured in a 6-well plate and incubated for 24 h for cell attachment, after which the medium was sucked and added with three concentrations (6, 8 and 10 μg/mL) of xanthone extracts or nanoemulsions for triplicate experiments. After incubation for 48 h, the medium was collected in a centrifuge tube and trypsin-EDTA (0.5 mL) added for incubating (37 °C) for 5–10 min. Following cell floating, the reaction was terminated with medium (0.5 mL), followed by the collection of cytosols in a centrifuge tube for centrifuging at 1500 rpm (25 °C) for 3 min, removal of the supernatant, addition of PBS (300 μL), addition of 720 μL of ethanol slowly, and storage at −20 °C overnight to fix cells. Following thawing, the cytosols were centrifuged again at 1500 rpm (4 °C) for 5 min, followed by removal of the supernatant, addition of PBS (0.5 mL), and centrifuging again using the same condition. Then, PBS (0.8 mL) was added, followed by addition of RNase A and propidium iodide for reaction in the dark (37 °C) for 30 min. for the determination of the proportions of Sub-G1, G0/G1, S and G2/M phases using Kuluza analysis software (version 3.1, Beckman Coulter Inc., Taipei, Taiwan).

Li R., Inbaraj B.S, & Chen B.H. (2023). Quantification of Xanthone and Anthocyanin in Mangosteen Peel by UPLC-MS/MS and Preparation of Nanoemulsions for Studying Their Inhibition Effects on Liver Cancer Cells. International Journal of Molecular Sciences, 24(4), 3934.

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Publication 2023

Cancer of Liver Cell-Matrix Junction Cells Cytosol Edetic Acid Ethanol G2 Phase Hepatocyte Homo sapiens Malignant Neoplasms Propidium Iodide Ribonucleases Trypsin xanthone

Cell Cycle Analysis of Plant Essential Oils

Analysis of cell cycle progression was assessed by flow cytometry using a PI/RNase solution (Immunostep, Salamanca, Spain), according to the manufacturer’s protocol. Briefly, cells were treated with two different concentrations (0.7 or 0.8 µL/mL) of either M. cervina EO or L. pedunculata EO and further incubated for 24 h. After incubation, cells were detached and fixed in 70% ethanol for 1 h at 4 °C. Then, cells were stained with 500 µL of PI/RNase solution. Results were acquired using CellQuest software and analyzed to calculate the percentage of the cell population in subG0/G1, G0/G1, S, and G2/M cell cycle phases.

Marques M.P., Neves B.G., Varela C., Zuzarte M., Gonçalves A.C., Dias M.I., Amaral J.S., Barros L., Magalhães M, & Cabral C. (2023). Essential Oils from Côa Valley Lamiaceae Species: Cytotoxicity and Antiproliferative Effect on Glioblastoma Cells. Pharmaceutics, 15(2), 341.

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Publication 2023

Cell Cycle Disease Progression Endoribonucleases Ethanol Flow Cytometry G2 Phase M Cells Pedunculata

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Propidium iodide is a fluorescent dye commonly used in molecular biology and flow cytometry applications. It binds to DNA and is used to stain cell nuclei, allowing for the identification and quantification of cells in various stages of the cell cycle.

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Flow cytometry by BD

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What is the G2 phase and why is it important for cell research?

The G2 phase is a critical stage in the cell cycle that occurs between the S phase and the M phase. During this phase, the cell prepares for mitosis by synthesizing the necessary proteins and organelles. The G2 phase is characterized by increased metabolic activity, DNA repair, and the assembly of the mitotic spindle. Optimizing G2 phase research is crucial for understanding cell division, development, and disease processes.

What are some common challenges researchers face when studying the G2 phase?

How can PubCompare.ai help researchers with their G2 phase research?

PubCompare.ai is an AI-driven platform that can assist researchers in optimizing their G2 phase research. The platform allows you to screen protocol literature more efficiently and leverage AI to pinpoint critical insights. PubCompare.ai's powerful comparison tools can help you identify the most reproducible and accurate protocols for your G2 phase research needs, saving you time and effort in the process.

What are the different variations or types of G2 phase research methods?

There are several variations of G2 phase research methods, including cell cycle synchronization techniques, live-cell imaging, and assays for measuring specific G2 phase markers and processes. Researchers may need to explore different approaches to study the G2 phase in their specific cell lines or experimental models. PubCompare.ai can assist in comparing the effectiveness of these various G2 phase research methods.

Can you provide some examples of how PubCompare.ai can be used for G2 phase research?

PubCompare.ai can be invaluble for G2 pahse research in several ways. For example, the platform can help researchers quickly identify the most effective protocols for synchronizing cells in the G2 phase, measuring G2 phase markers, or analyzing G2 phase-specific cellular processes. The AI-driven analysis can highlight key differences in protocol effectiveness, enabling researchers to choose the best option for their reproducibility and accuracy needs.

More about "G2 Phase"

The G2 phase, also known as the Gap 2 or Growth 2 phase, is a critical stage in the cell cycle that occurs between the S (Synthesis) phase and the M (Mitosis) phase.
During this phase, the cell prepares for cell division by synthesizing the necessary proteins and organelles required for successful mitosis.
The G2 phase is characterized by increased metabolic activity, DNA repair, and the assembly of the mitotic spindle, which is crucial for the proper segregation of chromosomes during cell division.
Optimizing G2 phase research is essential for understanding fundamental cellular processes, such as cell division, development, and disease mechanisms.
Researchers studying the G2 phase can utilize various techniques and instruments, including flow cytometry.
The FACSCalibur, a popular flow cytometer, can be used to analyze cell cycle progression and DNA content.
Propidium iodide, a fluorescent dye, can be used to stain DNA and determine the cell cycle stage.
The CycleTEST PLUS DNA Reagent Kit is designed to help researchers assess the cell cycle distribution.
Additionally, the FACScan flow cytometer and CellQuest software can be employed to acquire and analyze flow cytometry data related to the G2 phase.
RNase A, an enzyme that degrades RNA, can be used to improve the accuracy of DNA content analysis.
The FITC Annexin V Apoptosis Detection Kit can be utilized to study apoptosis, which may be associated with cell cycle regulation.
By leveraging these tools and techniques, researchers can gain valuable insights into the G2 phase and its role in cell division, development, and disease processes.
PubCompare.ai, an AI-driven platform, can help researchers identify the best scientific protocols from the literature, pre-prints, and patents, saving time and effort in their G2 phase research endeavors.