Log In Sign up
The largest database of trusted experimental protocols
> Chemicals & Drugs > Biologically Active Substance > Glycogen

Glycogen

Glycogen is a complex polysaccharide that serves as the primary storage form of glucose in the body.
It is found primarily in the liver and muscle cells, where it can be rapidly converted to glucose to meet the body's energy needs.
Glycogen plays a crucial role in maintaining blood glucose levels and providing a readily available source of energy for cellular processes.
Reseachers can leverage PubCompare.ai to optimize their glycogen research by identifying the most accurate and reproducilbe protocols from the literature, preprints, and patents.
This AI-driven platform enables them to compare methods and products, enhancing the quality and relaibility of their experiments.

Most cited protocols related to «Glycogen»

1
CEST Imaging of Glycogen Phantom and Calf Muscle
All images were acquired using a whole-body Philips 3T Achieva scanner (Philips Medical System, Best, The Netherlands) equipped with 80 mT/m gradients. RF was transmitted using the body coil and SENSE reception (31 (link)) was employed. A series of consecutive direct saturation and CEST scans were performed using the 8-element knee coil for both the glycogen phantom and in vivo human calf muscle. To minimize leg motion, foam padding was placed between the subject’s lower leg and the knee coil. In all cases, second order shims over the entire muscle on the imaging slice were optimized to minimize B0 field inhomogeneity. Notice that the width of Z-spectra depends on T2 and that the WASSR procedure provides an absolute field frequency map so that there is no need for higher order shimming for the CEST acquisition. Clinical imagers generally employ a prescan to center the bulk water signal of the object/subject, optimize the flip angle and shim the field. Note that no such “prescan” should be made between direct saturation and CEST scans to maintain the same field reference conditions. For both scans, saturation was accomplished using a rectangular RF pulse before the turbo spin echo (TSE) image acquisition, as previously described by Jones et al. (21 (link)).
The power level needed for each saturation experiment depended on the load and was optimized by measuring sets of Z-spectra under these different conditions. For WASSR, the power and pulse lengths were chosen as small as possible to have sufficient direct saturation, while minimizing any MT effects. For CEST, the maximum pulse length allowed for the body coil within the protected clinical software (500 ms) was used and the power was optimized for maximum effect at the phantom and muscle loads. WASSR was obtained at higher frequency resolution than CEST, but over a smaller frequency range as only the direct saturation region needs to be covered. The WASSR range was chosen sufficiently large to validate the simulated results, consequently leading to a larger number of frequencies needed in vivo than for the phantom.
Single-slice glycogen phantom imaging was performed using SENSE factor = 2, TSE factor [number of refocusing pulses] = 34 (two-shots TSE), TR = 3000 ms, TE = 11 ms, matrix = 128 × 122, FOV = 100 × 100 mm2, slice thickness = 5 mm, NSA = 1. Imaging parameters for human calf muscle experiments were identical to those in phantom experiments except for the following: FOV = 160 × 160 mm2. The saturation spectral parameters for WASSR and CEST are indicated in Table 1.
Kim M., Gillen J., Landman B.A., Zhou J, & van Zijl P.C. (2009). WAter Saturation Shift Referencing (WASSR) for chemical exchange saturation transfer experiments. Magnetic resonance in medicine : official journal of the Society of Magnetic Resonance in Medicine / Society of Magnetic Resonance in Medicine, 61(6), 1441-1450.
Publication 2009
Dietary Fiber ECHO protocol Glycogen Homo sapiens Human Body Knee Joint Leg Muscle Tissue Pulse Rate Pulses Radionuclide Imaging SHIMS
2
CUT&RUN Profiling of Transcription Factors and Histone Modifications
CUT&RUN was performed as previously described [10 (link)]. Briefly, cells were washed with Wash Buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine and one Roche Complete protein inhibitor tablet per 50 mL), bound to Concanavalin A-coated magnetic beads and incubated with primary antibody diluted in wash buffer containing 0.05% digitonin (Dig Wash) overnight at 4 °C. Cells were then washed and incubated with protein A-MNase (pA-MN) for 1 h at 4 °C. Slurry was washed again and placed on an ice-cold block and incubated with Dig Wash containing 2 mM CaCl2 to activate pA-MN digestion. After digestion for 30 min, one volume of 2× stop buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.05% Digitonin, 0.05 mg/mL glycogen, 5 µg/mL RNase A, 2 pg/mL heterologous spike-in DNA) was added to stop the reaction, and fragments were released by 30-min incubation at 37 °C. Samples were centrifuged 5 min at 16,000×g, and supernatant was recovered and DNA extracted via phenol–chloroform extraction and ethanol precipitation. Resulting DNA was used as input for library preparation as previously described [10 (link)]. Antibodies used for CUT&RUN in this study were as follows: rabbit anti-Sox2 (Abcam ab92494); rabbit anti-FoxA2 (Millipore 07-633); Guinea-Pig anti-rabbit IgG (antibodies online ABIN101961); rabbit anti-H3K4me2 (Millipore 07-030); rabbit anti-H3K4me3 (Active Motif 39159); rabbit anti-H3K27me3 (Cell Signaling Technologies CST9733); and rabbit anti-CTCF (Millipore 07-729).
Meers M.P., Tenenbaum D, & Henikoff S. (2019). Peak calling by Sparse Enrichment Analysis for CUT&RUN chromatin profiling. Epigenetics & Chromatin, 12, 42.
Full text: Click here
Publication 2019
anti-IgG Antibodies Buffers Cavia porcellus Cells Chloroform Cold Temperature Concanavalin A CTGF protein, human Digestion Digitonin DNA Library Edetic Acid Egtazic Acid Ethanol Glycogen HEPES histone H3 trimethyl Lys4 Immunoglobulins Phenol Protein Digestion Proteins Rabbits Ribonucleases Sodium Chloride SOX2 protein, human Spermidine Staphylococcal Protein A Tablet
3
Lipid and Glycogen Quantification in Larvae

Protocol full text hidden due to copyright restrictions

Open the protocol to access the free full text link

Publication 2009
Animals Biological Assay Dissection Formaldehyde Glucan 1,4-alpha-Glucosidase Glucose Glycerin Glycogen Larva Microscopy Microscopy, Confocal Propylene Glycol Proteins solvent red 27 Staining Student Triglycerides Tween 20
4
CEST-FISP Glycogen Imaging Protocol
A CEST-FISP pulse sequence was developed on a Bruker Biospec 7.0T MRI scanner (Bruker Biospin, Billerica, MA) by combining a train of spectrally-selective CEST excitation pulses with a FISP acquisition scheme (Figure 1). The CEST preparation was developed with a train of 120 spectrally-selective Gaussian saturation pulses (BWRF = 75 Hz, TauRF = 36 ms). Gradient spoilers were applied following each CEST pulse to avoid unintended buildup of transverse magnetization. These conditions resulted in a total CEST preparation period of approximately 5 seconds immediately prior to the imaging readout (18 (link)). This CEST pulse train was developed to provide a flexible CEST preparation sensitive to glycogen exchange in order to evaluate the fundamental characteristics of the CEST-FISP technique. As such, this CEST preparation was not optimized for this specific application.
The CEST preparation above was coupled with a conventional FISP acquisition to acquire all lines of k-space following a single CEST preparation. A FISP acquisition was used instead of a True FISP acquisition to avoid well-known banding artifacts resulting from B0 inhomogeneities at 7.0T (16 ,17 ). For all in vitro experiments, the imaging parameters were FISP Repetition Time = 2ms, echo time = 1 ms, matrix = 128×92, FOV = 6×4 cm, slice thickness = 2 mm (single-slice), flip angle = 60°, and readout bandwidth = 600 kHz. Ten dummy scans were utilized to limit artifacts from the approach to steady-state. The total duration of the dummy scans was < 30ms and centric encoding was implemented for the FISP acquisition to minimize the loss of CEST sensitivity following the CEST preparation.
Shah T., Lu L., Dell K., Pagel M., Griswold M, & Flask C. (2010). CEST-FISP: A Novel Technique for Rapid Chemical Exchange Saturation Transfer (CEST) MRI at 7T. Magnetic resonance in medicine : official journal of the Society of Magnetic Resonance in Medicine / Society of Magnetic Resonance in Medicine, 65(2), 432-437.
Publication 2010
ECHO protocol Glycogen Hypersensitivity interleukin-24 Neoplasm Metastasis Pulse Rate Pulses Radionuclide Imaging
5
Xenopus Egg Extract DNA Replication

Protocol full text hidden due to copyright restrictions

Open the protocol to access the free full text link

Publication 2008
Chloroform DNA Replication Edetic Acid Endopeptidase K Ethanol Gels Glycogen Phenol Plasmids Ribonucleases Sepharose Tromethamine Xenopus laevis

Most recents protocols related to «Glycogen»

1
Single-Cell Genomic DNA Assay
Not available on PMC !

Example 3

Genomic DNA is assayed as a proof of concept for assaying RNA, as it provides a way to establish a single-copy reference signal. Once a working assay is developed for FFPE samples, it is adapted to an RNA assay. To this end, assay oligonucleotide concentrations are assayed to ensure compatibility with high multiplexing. Assuming a cell diameter of 10 microns, and delivery of a 10 micron diameter reagent droplet to an individual cell, the volume of the droplet will be ˜500 μl and can contain ˜3×1011 molecules at a concentration. To assay 1,000 target sequences in 10,000 cells, 2,000 targeting oligonucleotides would be required in a droplet. Therefore, each droplet could contain ˜160 million copies of each assay oligo, a vast excess over the few thousand target sequences in a cell.

The handling of small absolute numbers of product molecules generated from very small or compromised samples are enhanced to counter the issue of low recovery efficiency; that is, elution is efficient and losses resulting from adsorption of molecules to surfaces are prevented. An approach to addressing the latter issue is to include a carrier material, such as glycogen or carrier nucleic acids.

US11866770B2. Spatially encoded biological assays (2024-01-09). Prognosys Biosciences, Inc. [US]. Inventors: Mark S. Chee [US].
Full text: Click here
Patent 2024
Acclimatization Adsorption Biological Assay Cells Genome Glycogen Nucleic Acids Obstetric Delivery Oligonucleotides
2
Genome-wide Chromatin Profiling by ChIP-seq and ATAC-seq
Chromatin immunoprecipitation (ChIP) and Assay for Transposase-Accessible Chromatin (ATAC) sequencing was performed as previously described36 (link). For ChIP-seq a total of 10 × 107 cells were crosslinked with 1% formaldehyde while shaking for 7 min at room temperature, quenched with 125 mM glycine, lysed and sonicated with the S2 Covaris for 30 min to obtain 200–300 bp long fragments. Chromatin fragments were immunoprecipitated overnight using 1 µg antibody of SOX11-PAb antibody (custom made by Absea biotechnology, China) and 20 µl Protein A UltraLink® Resin (Thermo Scientific, #53139) beads per 10 × 107 cells. Reverse crosslinking was done at 65 °C for 15 h and chromatin was resuspended in TE-buffer, incubated for 2 h at 37 °C with 0.2 mg/ml RNase and followed by an incubation of 2 h at 55 °C with 0.2 mg/ml proteinase K. DNA was isolated using 400 µl phenol:chloroform:isoamylalcohol (P:C:IA) in phase lock gel tubes (5Prime). Upon centrifugation, the aqueous layer was transferred to a new tube with 200 mM NaCl, 30 µg glycogen and 800 µl 100% ethanol, and incubated for 30 min at −20 °C. Upon centrifugation, the pellet was washed with 80% Ethanol and resuspended in RNase/DNase free water. DNA concentration was measured using the Qubit® dsDNA HS Assay Kit. Library prep was done using the NEBNExt Ultra DNA library Prep Kit for Illumina (E7370S) with 500 ng starting material and using 8 PCR cycles according to the manufacturer’s instructions. For ATAC-seq, 50,000 cells were lysed and fragmented using digitonin and Tn5 transposase. The transposed DNA fragments were amplified and purified using Agencourt AMPure XP beads (Beckman Coulter). ChIP and ATAC library concentrations were measured with the Illumina Kapa Library quantification kit (Roche #07960140001) and libraries were sequenced on the NextSeq 500 (Illumina) using the Nextseq 500 High Output kit V2 75 cycles single-end (Illumina).
Decaesteker B., Louwagie A., Loontiens S., De Vloed F., Bekaert S.L., Roels J., Vanhauwaert S., De Brouwer S., Sanders E., Berezovskaya A., Denecker G., D’haene E., Van Haver S., Van Loocke W., Van Dorpe J., Creytens D., Van Roy N., Pieters T., Van Neste C., Fischer M., Van Vlierberghe P., Roberts S.S., Schulte J., Ek S., Versteeg R., Koster J., van Nes J., Zimmerman M., De Preter K, & Speleman F. (2023). SOX11 regulates SWI/SNF complex components as member of the adrenergic neuroblastoma core regulatory circuitry. Nature Communications, 14, 1267.
Full text: Click here
Publication 2023
AT 125 ATAC-Seq Biological Assay Buffers Cells Centrifugation Chloroform Chromatin Deoxyribonucleases Digitonin DNA, Double-Stranded DNA Library Ethanol Formaldehyde Glycine Glycogen Immunoglobulins Immunoprecipitation, Chromatin Phenol proteinase C Resins, Plant ribonuclease C Ribonucleases Sodium Chloride SOX11 protein, human Staphylococcal Protein A Tn5 transposase Transposase XCL1 protein, human
3
DNA Extraction and Restriction Analysis
H2O was added to the DNA samples taken during the purification process to a final volume of 100μL. 1ng of plasmid K71 was also added to every sample as a spike-in to normalize for different DNA extraction efficiencies. 100μL of IRN buffer (50mM Tris-HCl pH8, 20mM EDTA, 0.5M NaCl, 0.5% SDS, 10μL Proteinase K (10 mg/mL) were added together with 1μL of RNAse A (10 mg/mL), followed by a 1h incubation step at 37°C. Subsequently, 200μL Phenol:Chloroform:Isoamyl Alcohol (25:24:1, v/v) was added, followed by 2 × 10sec thorough vortexing. The solution was centrifuged for 5 min at 16.000g. The supernatant was transferred to a fresh 1.5mL tube containing 600μL of ethanol and 1.5μL glycogen (10 mg/mL). The tube was left at −20°C overnight. Next, the solution was centrifuged with 16.000 g at 4°C for 30min. The supernatant was discarded and 150μL of 70% ethanol was added to the pellet. After another centrifugation step with 16.000 g at 4°C for 10min, the supernatant was discarded and the DNA pellet dried at room temperature for 10min. The dried pellet was then resuspended in 50μL H2O. For further analysis, a restriction digestion was performed to analyze the DNA samples in subsequent qPCR reactions. The restriction enzymes used for linearizing the circular DNA were HpaI (ARS305+/−3), BbsI (ARS313+/−3), NcoI (ARS315+/−3) and HpaI (ARS316+/−3). qPCR analysis was performed using the following primer pairs: ARS305: 0463/0466; ARS313: 0552/0553; ARS315: 0970/0971; ARS316: 0837/0838. Primers 0137 and 0138 are used to detect the K71 spike-in and primers 0301 and 0302 were used to detect the unrelated genomic PDC1 locus.
Weiβ M., Chanou A., Schauer T., Tvardovskiy A., Meiser S., König A.C., Schmidt T., Kruse E., Ummethum H., Trauner M., Werner M., Lalonde M., Hauck S.M., Scialdone A, & Hamperl S. (2023). Single-copy locus proteomics of early- and late-firing DNA replication origins identifies a role of Ask1/DASH complex in replication timing control. Cell Reports, 42(2), 112045.
Full text: Click here
Publication 2023
Buffers Centrifugation Chloroform Digestion DNA, Circular DNA Restriction Enzymes Edetic Acid Endopeptidase K Endoribonucleases Ethanol Genome Glycogen isopentyl alcohol Oligonucleotide Primers Phenol Plasmids Sodium Chloride Tromethamine
4
Selective Extraction and Detection of HBV cccDNA
To selectively extract HBV cccDNA, infected HepG2-NTCP cells were lysed in 6-cm dishes with 1 mL of lysis buffer at 37°C for 60 min, and then, incubated with 0.25 mL of 2.5 M KCl overnight at 4°C. The lysis buffer contained 50 mM Tris–HCl (pH 7.4), 10 mM EDTA, 150 mM NaCl, and 1% SDS, without proteinase K. The lysate was clarified by centrifugation at 12,000 g for 30 min at 4°C. Viral DNA was extracted with phenol and phenol: chloroform, precipitated in an equal volume of isopropanol containing 20 µg glycogen (Roche), and dissolved in TE buffer. The prepared DNA sample was then treated with plasmid-safe adenosine triphosphate (ATP)-dependent deoxyribonuclease DNase (Epicentre Technologies) following the manufacturer’s instructions.
The treated Hirt DNA was subjected to Taq-man probe RT-qPCR for detecting the HBV cccDNA levels; the specific primers and the probe used are listed in the Supplementary (Table. S1).
Cai J., Li Y., Hu P., Xu R., Yuan H., Zhang W., Feng T., Liu R., Li W, & Zhu C. (2023). Plerixafor and resatorvid inhibit hepatitis B virus in vitro by upregulating elongation factor Tu GTP-binding domain containing 2. Frontiers in Cellular and Infection Microbiology, 13, 1118801.
Full text: Click here
Publication 2023
Adenosine Triphosphate Buffers Centrifugation Chloroform Deoxyribonucleases DNA, Viral Edetic Acid Endopeptidase K Glycogen Hep G2 Cells Hyperostosis, Diffuse Idiopathic Skeletal Isopropyl Alcohol Oligonucleotide Primers Phenols Plasmids Sodium Chloride Tromethamine
5
Optimized RNA Extraction from Extracellular Vesicles
For RNA including miRNA purifications, SF-EVs (n = 70) and SF-Native (n = 70) samples were mixed with 600 µl QIAzol Lysis Reagent (Qiagen) and 100 µl Dithiothreitol (0.1 M, DTT) (Sigma–Aldrich). Samples were incubated for 5 min at RT and then 140 µl of chloroform was added, vortexed, and incubated for an additional 3 min at RT. The mixture was then centrifuged at 4 °C for 20 min at 14,000 × g, 12 µl glycogen (5 ng/µl) (Thermo Fisher Scientific) was added to each collected supernatant, and miRNeasy® Mini (Qiagen) Kit was used to purify the RNA including miRNAs. Elution was performed with 15 µl of RNase-free water and quantification was performed using NanoDrop™ 2000c Spectrophotometers (Thermo Fisher Scientific). RNA quality was randomly checked using a Bioanalyzer 2100 instrument (Agilent Technologies).
Abu-Halima M., Becker L.S., Al Smadi M.A., Kunz L.S., Gröger L, & Meese E. (2023). Expression of SPAG7 and its regulatory microRNAs in seminal plasma and seminal plasma-derived extracellular vesicles of patients with subfertility. Scientific Reports, 13, 3645.
Full text: Click here
Publication 2023
Chloroform Dithiothreitol Endoribonucleases Glycogen MicroRNAs

Top products related to «Glycogen»

1
Glycogen by Thermo Fisher Scientific
Sourced in United States, Germany, Lithuania, Australia, Switzerland
Glycogen is a complex carbohydrate that serves as a storage form of glucose in the body. It is primarily found in the liver and muscle tissues of various organisms. Glycogen can be broken down into glucose units when the body requires energy, making it a crucial component in energy metabolism.
2
Trizol reagent by Thermo Fisher Scientific
Sourced in United States, China, Japan, Germany, United Kingdom, Canada, France, Italy, Australia, Spain, Switzerland, Netherlands, Belgium, Lithuania, Denmark, Singapore, New Zealand, India, Brazil, Argentina, Sweden, Norway, Austria, Poland, Finland, Israel, Hong Kong, Cameroon, Sao Tome and Principe, Macao, Taiwan, Province of China, Thailand
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.
3
Trizol by Thermo Fisher Scientific
Sourced in United States, Germany, China, Japan, United Kingdom, Canada, France, Italy, Australia, Spain, Switzerland, Belgium, Denmark, Netherlands, India, Ireland, Lithuania, Singapore, Sweden, Norway, Austria, Brazil, Argentina, Hungary, Sao Tome and Principe, New Zealand, Hong Kong, Cameroon, Philippines
TRIzol is a monophasic solution of phenol and guanidine isothiocyanate that is used for the isolation of total RNA from various biological samples. It is a reagent designed to facilitate the disruption of cells and the subsequent isolation of RNA.
4
Glycogen assay kit by Abcam
Sourced in United States, United Kingdom, Japan
The Glycogen Assay Kit is a laboratory tool used to quantify the amount of glycogen present in biological samples. It provides a colorimetric method for the direct determination of glycogen levels.
5
Amyloglucosidase by Merck Group
Sourced in United States, Germany, China, Ireland, Japan, United Kingdom, Switzerland, Sao Tome and Principe, Australia, India
Amyloglucosidase is an enzyme that hydrolyzes starch and glycogen to glucose. It is commonly used in the food and beverage industry for the production of glucose syrups and other sweeteners.
6
Glycogen by Roche
Sourced in Germany
Glycogen is a complex carbohydrate molecule that serves as the primary storage form of glucose in the body. It is found predominantly in the liver and skeletal muscles, where it can be readily converted into glucose to provide energy for cellular processes.
7
Glycogen by Merck Group
Sourced in United States, Germany
Glycogen is a complex carbohydrate that serves as a storage form of glucose in the body. It is primarily found in the liver and muscles, where it can be rapidly converted back into glucose for energy when needed. Glycogen is an important component in various biological processes and has applications in laboratory settings, but a detailed description of its functions and intended uses would require more specialized expertise.
8
Glycogen assay kit by Merck Group
Sourced in United States, Germany
The Glycogen Assay Kit is a laboratory product that provides a quantitative method for the determination of glycogen levels in various biological samples. The kit includes the necessary reagents and protocols to accurately measure glycogen concentrations.
9
Agilent 2100 bioanalyzer by Agilent Technologies
Sourced in United States, Germany, Canada, China, France, United Kingdom, Japan, Netherlands, Italy, Spain, Australia, Belgium, Denmark, Switzerland, Singapore, Sweden, Ireland, Lithuania, Austria, Poland, Morocco, Hong Kong, India
The Agilent 2100 Bioanalyzer is a lab instrument that provides automated analysis of DNA, RNA, and protein samples. It uses microfluidic technology to separate and detect these biomolecules with high sensitivity and resolution.
10
Trizol ls by Thermo Fisher Scientific
Sourced in United States, Germany, United Kingdom, Canada, Australia, Japan, France, China
TRIzol LS is a guanidinium-based reagent used for the isolation of total RNA from various samples, including liquid samples. It is designed to effectively lyse cells and solubilize cellular components while maintaining the integrity of the extracted RNA.

More about "Glycogen"

Glycogen, the complex polysaccharide that serves as the primary storage form of glucose in the body, plays a crucial role in maintaining blood glucose levels and providing a readily available source of energy for cellular processes.
Found primarily in the liver and muscle cells, glycogen can be rapidly converted to glucose to meet the body's energy needs.
Researchers can leverage PubCompare.ai, an AI-driven platform, to optimize their glycogen research by identifying the most accurate and reproducbile protocols from the literature, preprints, and patents.
This platform enables researchers to compare methods and products, enhancing the quality and reliability of their experiments.
TRIzol reagent, a popular RNA extraction solution, and the TRIzol LS variant for liquid samples, can be used in conjunction with glycogen to improve RNA isolation and purification.
The Glycogen Assay Kit, on the other hand, provides a convenient way to quantify glycogen levels in biological samples.
Amyloglucosidase, an enzyme that catalyzes the hydrolysis of glycogen, can be utilized to analyze glycogen content.
Additionally, the Agilent 2100 Bioanalyzer, a microfluidics-based platform, can be employed to assess the quality and quantity of glycogen-related biomolecules.
By leveraging these tools and techniques, researchers can optimize their glycogen research, leading to more accurate and reliable results.
PubCompare.ai offers a powerful solution to streamline this process, helping scientists navigate the vast landscape of glycogen-related literature, preprints, and patents.