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Phenols

Phenols are a class of organic compounds containing a hydroxyl group (-OH) attached to an aromatic ring.
These compounds are widely distributed in nature and have diverse biological and industrial applications.
Phenols exhibit a variety of chemical and physical properties, including antimicrobial, antioxidant, and pollution-reducing activities.
Research in phenols is crucial for understanding their role in various fields, such as pharmacology, environmental science, and material science.
PubCompare.ai provides an AI-driven platform to optimize your phenols research workflow, enabling you to locate the best published, preprint, and patent procedures, while enhancing reproducibility and accuracy.
Leverge our unique platform to elevate your phenols studies and drive innovation.

Most cited protocols related to «Phenols»

ES cells and ES-derived neural cells were cultured as described previously11 (link),25 (link). Primary tissues were isolated from 4–6-week-old male 129SvJae/C57/B6 mice. Mouse embryonic fibroblasts (MEFs) and primary neural precursors were isolated from 129SvJae/C57/B6 E14.5 embryos.
RRBS libraries were prepared from 1–10 μg mouse genomic DNA digested with 10–100 Units MspI (NEB). Size-selected MspI fragments (40–120 bp and 120–220 bp) were filled in and 3′-terminal-A extended, extracted with phenol and precipitated with ethanol. Ligation to pre-annealed adapters containing 5′-methyl-cytosine instead of cytosine (Illumina) was performed using the Illumina DNA preparation kit and protocol. QIAquick (Qiagen) cleaned-up, adaptor-ligated fragments were bisulphite-treated using the EpiTect Bisulphite Kit (Qiagen). Preparative-scale PCR was performed and QIAquick-purified PCR products were subjected to a final size selection on a 4% NuSieve 3:1 agarose gel. SYBR-green-stained gel slices containing adaptor-ligated fragments of 130–210 bp or 210–310 bp in size were excised. Library material was recovered from the gel (QIAquick) and sequenced on an Illumina 1G genome analyser.
Sequence reads from bisulphite-treated Solexa libraries were identified using standard Illumina base-calling software and then analysed using a custom computational pipeline. ChIP-Seq experiments, sequencing, alignments and identification of significantly enriched regions were carried out as described previously11 (link).
Publication 2008
5-Methylcytosine Chromatin Immunoprecipitation Sequencing Embryo Embryonic Stem Cells Ethanol Fibroblasts Genome hydrogen sulfite Ligation Males Mice, House Nervousness Neurons Phenols Sepharose SYBR Green I Tissues
Caenorhabditis sp. 5 (strain JU800) DNA was provided by Asher Cutter (University of Toronto). The DNA was extracted from a sucrose- and detergent-cleaned plate culture of nematodes using proteinase K and phenol–chloroform. The standard Illumina protocol was used to generate two libraries with fragment sizes 300 and 600 bp and sequenced on an Illumina HiSeq2000 instrument using 101 base, paired-end sequencing with V3 reagents. Raw sequence data are available at the Short Read Archive with accession number ERP001495. Raw reads were adapter- and quality-trimmed using fastq-mcf (Aronesty, 2011 ; Table 1) with a trimming threshold quality of 20, discarding reads shorter than 50 b. A total of 136.3 M read pairs totaling 26.9 Gb remained after these trimming steps (Table 2). A full analysis of the genome of Caenorhabditis sp. 5 will be published elsewhere. The Dirofilaria immitis sequencing data have been described previously (Godel et al., 2012 (link)).
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Publication 2013
Caenorhabditis Chloroform Detergents Dirofilaria immitis Endopeptidase K Genome Nematoda Phenols Strains Sucrose
The genomic DNA was extracted from 200 μl blood samples with the QIAamp DNA Blood Mini kit (Qiagen) and from the skin samples with a standard phenol–chloroform method. The quality and integrity of DNA was controlled by OD260/280 ratio and agarose gel electrophoresis. For sequencing library preparation, the genomic DNA was sheared to fragments of 300–500 bp, which were then end repaired, ‘A’-tailed, and ligated to Illumina sequencing adapters. The ligated products with sizes of 370–470 bp were selected on 2% agarose gels and then amplified by PCR. The libraries were sequenced on Illumina HiSeq platform with standard paired-end mode.
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Publication 2020
BLOOD Chloroform DNA Library Electrophoresis, Agar Gel Gels Genome Phenols Sepharose Skin
Twenty-seven colon cancer cell lines were initially included in the present study. HCT-116, HCT-15, LoVo, RKO, SW1116, SW48, SW620, SW948, NCI-H508 and WiDr were purchased from the American Type Culture Collection (ATCC, Manassas, VA, USA). ALA, CaCo-2, CO-115, COLO 320, DLD-1, EB, FRI, HT-29, IS1, IS2, IS3, LS1034, LS-174T, TC7, TC71, SW480 and V9P were kindly provided by collaborators. Cell lines were cultured in medium with added fetal bovine serum, glutamine, penicillin and streptomycin, and were maintained in humidified 37 °C 5% CO2 incubators as described in Supplementary Table 2. Before collection, cultures were tested for mycoplasma infection using Myco Alert (Lonza, Walkersville, MD, USA) according to the manufacturer's protocol.
DNA was isolated using either a standard phenol/chloroform procedure, or a magnetic beads approach (the Maxwell 16 DNA Purification kits, Promega Corporation, Madison, WI, USA, and MagAttract DNA Mini M48 kit, Qiagen Inc., Valencia, CA, USA). DNA was STR profiled using the AmpFLSTR Identifiler PCR Amplification Kit (Life Technologies, Carlsbad, CA, USA). Resulting cancer cell line STR profiles were cross-compared and, where available, matched with the ATCC's and German Collection of Microorganisms and Cell cultures' (Braunschweig, Germany) online databases. Hierarchical clustering of STR data was performed using Euclidian distances and average linkage clustering in Partek Genomics Suite 6.6 (Partek Inc., St Louis, MO, USA; Figure 2). ALA, CO-115, EB, FRI, IS1, IS2, IS3, TC7, TC71 and V9P are non-commercial cell lines and their STR profiles will be provided upon request. Three of the 27 cancer cell lines were found to be misclassified. ALA and IS2 had identical profiles to SW480/SW620 and LS1034, respectively. TC7 had a STR profile incompatible with its origin as a Caco-2 subclone.41 Consequently, ALA, IS2 and TC7 were excluded from further analysis.
Micrographs of live cell cultures were captured with an Eclipse TS100 microscope equipped with a × 10 phase-contrast objective using accompanying NIS-Elements F Package 2.21 software (all from Nikon, Tokyo, Japan). Resulting images were imported into Photoshop CS4 (Adobe Systems, Mountain View, CA, USA), cropped and color matched.
Publication 2013
Cancer of Colon Cell Culture Techniques Cell Lines Chloroform Fetal Bovine Serum Glutamine HT29 Cells Malignant Neoplasms Microscopy Microscopy, Phase-Contrast Mycoplasma Infections Penicillins Phenols Promega Reproduction Streptomycin
Sequence tag preparation was done with Illumina's Digital Gene Expression Tag Profiling Kit according to the manufacturer's protocol (version 2.1B). A schematic overview of the procedure is given in Supplementary Figure 1. One microgram of total RNA was incubated with oligo-dT beads to capture the polyadenlyated RNA fraction. First- and second-strand cDNA synthesis were performed while the RNA was bound to the beads. While on the beads, samples were digested with NlaIII to retain a cDNA fragment from the most 3′ CATG to the poly(A)-tail. Subsequently, the GEX adapter 1 was ligated to the free 5′ end of the RNA, and a digestion with MmeI was performed, which cuts 17 bp downstream of the CATG site. At this point, the fragments detach from the beads. After dephosphorylation and phenol extraction, the GEX adapter 2 was ligated to the 3′ end of the tag. A PCR amplifcation with 15 cycles using Phusion polymerase (Finnzymes) was performed with primers complementary to the adapter sequences to enrich the samples for the desired fragments. The resulting fragments of 85 bp were purified by excision from a 6% polyacrylamide TBE gel. The DNA was eluted from the gel debris with 1× NEBuffer 2 by gentle rotation for 2 h at room temperature. Gel debris were removed using Spin-X Cellulose Acetate Filter (2 ml, 0.45 µm) and the DNA was precipitated by adding 10 µl of 3 M sodium acetate (pH 5.2) and 325 µl of ethanol (–20°C), followed by centrifugation at 14 000 r.p.m. for 20 min. After washing the pellet with 70% ethanol, the DNA was resuspended in 10 µl of 10 mM Tris–HCl, pH8.5 and quantified the DNA with a Nanodrop 1000 spectrophotometer.
Publication 2008
acetylcellulose Anabolism Centrifugation DNA, Complementary Ethanol Fingers oligo (dT) Oligonucleotide Primers Pepsin A Phenols Poly(A) Tail polyacrylamide gels Sodium Acetate Strains Tromethamine

Most recents protocols related to «Phenols»

Example 1

Monomer M-1 was prepared by mixing 2-(dimethylamino)ethyl methacrylate with pentafluorobenzoic acid in a molar ratio of 1:1. Similarly, Monomers M-2 to M-17 and cM-1 were prepared by mixing a nitrogen-containing monomer with a fluorinated carboxylic acid, fluorinated sulfonamide compound, fluorinated phenol compound, fluorinated β-diketone compound, or unsubstituted benzoic acid (for comparison).

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[2] Synthesis of Polymers

Fluorine-containing monomers FM-1 to FM-11 and PAG monomer PM-1 used in the synthesis of polymers have the structure shown below.

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Patent 2024
Anabolism Benzoic Acid ethylmethacrylate Fluorine Molar Nitrous Acid pentafluorobenzoic acid Phenols Polymers Sulfonamides
Microscopy was performed using a Quorum Diskovery microscope that is comprised of a Leica DMi8 microscope equipped with a 63×/1.49 NA TIRF objective with a 1.8× camera relay (total magnification 108×). Imaging was done using 488-, 561, and 637-nm laser illumination and 527/30, 630/75, and 700/75 emission filters. The microscope was operated in TIRFM or widefield epifluorescence microscopy modes, as indicated. Images were acquired using a Zyla 4.2Plus sCMOS camera (Hamamatsu). Fixed-cell TIRFM imaging was done at room temperature with samples mounted in PBS. For live-cell imaging experiments (Figs. 1 and 2), cells were maintained at constant 37 °C during imaging, in phenol-free DMEM/F12 media (Gibco) supplemented with 20 mM Hepes.
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Publication 2023
Cells Figs HEPES Light Microscopy Phenols
Blood samples were collected from five male Labeo rohita (henceforth referred to as Rohu-1 through Rohu-5) from a fish farm located in the District of Rangpur, Bangladesh. The fish were handled as per guidelines of the Ethics Standard Review Committee of Bangladesh Agricultural University (BAU) involving fish and animals (approval no. BAURES/ESRC/2019/Fish/01). Each fish was euthanized using clove oil, dissected, and blood was collected from the heart using a syringe. Each blood sample was placed in an ethylenediaminetetraacetic acid containing vial, and vials were shipped in an insulated container to Mississippi State University for DNA extraction.
High-molecular-weight (HMW) genomic DNA for whole genome sequencing was extracted from 150 µl of blood from Rohu-1 using CTAB lysis buffer followed by the phenol/chloroform purification procedure (Doyle and Doyle 1987 ). The concentration and purity of extracted genomic DNA samples were measured by a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). The quality of genomic DNA was validated by electrophoresis on a 0.8% w/v agarose gel.
The genomic DNA from Rohu-1 was used to prepare 10 Oxford Nanopore R9.4 MinION flow cells. For each flow cell, 2 to 2.5 µg of genomic DNA and a Nanopore Genomic DNA Ligation Sequencing Kit SQK-LSK 109 (Oxford Nanopore Technologies, Oxford, UK) were used to create a DNA library. For each of the 10 libraries, 700–750 ng of DNA was loaded onto a Nanopore Flow Cell R9.4.1 (Oxford Nanopore Technologies, Oxford, UK) and sequenced on a GridION sequencer (Oxford Nanopore Technologies, Oxford, UK) for 48 h.
Rohu-1 genomic DNA was also sequenced on an Illumina HiSeq X-Ten (2 × 150 bp). In brief, 2 µg of Rohu-1 genomic DNA was used with an Illumina TruSeq DNA PCR-free Library Prep Kit (Illumina, San Diego, CA, USA) to create an Illumina sequencing library. The final DNA-Seq library, which had an insert size range of 350–450 bp, was submitted to Novogene (www.en.novogene.com) for two lanes of PE150 on an Illumina HiSeq X-Ten (Illumina, San Diego, CA, USA) sequencer.
A Hi-C library also was prepared using 100 µl of Rohu-1 blood with the Proximo Hi-C Animal Kit (Phase Genomics, Seattle, WA, USA). The final Hi-C DNA-Seq library was submitted to Novogene (www.en.novogene.com) for one lane of PE150 Illumina HiSeq X-Ten (Illumina, San Diego, CA, USA) sequencing.
Lastly, Rohu-1 blood cells were embedded in agarose and HMW DNA was isolated according to the Bionano Prep Frozen Blood Protocol (Bionano Genomics, San Diego, CA) . The extracted DNA molecules were labeled with the Direct Label and Stain (DLS) DNA Labeling kit (Bionano Genomics, San Diego, CA). Once labeled and stained, the DNA was imaged on the Bionano Saphyr instrument (Bionano Genomics, San Diego, CA).
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Publication 2023
Animals BLOOD Blood Cells Buffers Cells Cetrimonium Bromide Chloroform DNA, A-Form DNA Library Edetic Acid Electrophoresis Ethics Committees Fishes Freezing Genome H-DNA Heart Ligation Males Oil, Clove Phenols Sepharose Syringes
The GSE113725 dataset downloaded from the GEO database contained the DNA methylation data of adult MDD patients and HCs. This experiment used a standard phenol-chloroform extraction method to isolate genomic DNA from whole blood, and the samples were processed in accordance with the Illumina Infinium HumanMethylation450K BeadChip (Illumina). For the purpose of this study, we extracted the clinical information data and DNA methylation expression data of 49 adult MDD patients and 48 adult HCs. We used the same method to process the methylation data and then analyzed the differential DNA methylation positions between the two groups according to p < 0.01. Then, we used ggplot2 to draw a volcano plot and heatmap of differentially expressed DNA methylation positions. Then GO and KEGG enrichment analysis were performed.
We searched for the intersection of differentially expressed mRNAs and DNA methylation positions between our clinical data and GEO database, and compared their GO and KEGG results.
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Publication 2023
Adult BLOOD Chloroform DNA Methylation Genome Methylation Patients Phenols RNA, Messenger
Fecal samples from 12-week-old mice were collected and stored at −20°C. Bacterial DNA was extracted as previously described (31 (link)). Briefly, fecal samples were resuspended in 300 µl TE buffer (10 mM Tris and 1 mM EDTA, pH 8) containing 7.5 µl SDS (0.5%) and 3 µl proteinase K (20 mg/ml) and incubated for 1 hour at 37°C (all Sigma-Aldrich). One volume of phenol/chloroform/isoamyl alcohol (25:24:1), 200 µl of 20% SDS, and 0.3 g of zirconium/silica beads (0.1 mm; BioSpec, Bartlesville, OK, USA) were added, and samples were mixed with a Mini bead-beater (BioSpec) for 2 min. The samples were then mixed with 820 µl phenol/chloroform/isoamyl alcohol (25:24:1) and centrifuged, and the aqueous layer was collected into a new tube. The bacterial DNA was precipitated with 0.6 volume of isopropanol, washed with 70% ethanol, air dried, and resuspended in 100 µl of sterile water. The V4 region of the bacterial 16S ribosomal gene was amplified from each DNA sample with barcoded broadly conserved bacterial primers (forward (5′-GTGCCAGCMGCCGCGGTAA-3′) and reverse primer (5′-GGACTACHVGGGTWTCTAAT-3′)). The PCR products were purified with a gel extraction kit (QIAGEN) and quantified with a spectrophotometer (Nanodrop), and equimolar amounts of each sample were pooled and pyrosequenced on an Ion Torrent personal genome machine sequencing system (Thermo Fisher Scientific). The results were analyzed using the QIIME software package (version 1.8) and UPARSE pipeline (version 7.0). After removing the primer sequences, the sequences were demultiplexed, quality filtered using QIIME, and further quality and chimera filtered in UPARSE pipeline. Operational taxonomic units (OTUs) were picked with 97% identity in UPARSE pipeline. In QIIME, the Greengenes reference database was used for taxonomy assignment, which was performed at various levels using representative sequences of each OTU. β-Diversity was calculated to compare differences between microbial community profiles, and the data are shown as a principal coordinate analysis (PCoA).
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Publication 2023
Bacteria Buffers Chimera Chloroform DNA, Bacterial Edetic Acid Endopeptidase K Ethanol Feces Genes, Bacterial Genome isopentyl alcohol Isopropyl Alcohol Mice, House Microbial Community Oligonucleotide Primers Phenols Ribosomes Silicon Dioxide Sterility, Reproductive Tromethamine Zirconium

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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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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.
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The NanoDrop spectrophotometer is a compact and efficient instrument designed for the measurement of small-volume samples. It utilizes a patented sample-retention technology to enable accurate and reproducible spectroscopic analyses of various biomolecules, including nucleic acids and proteins, in a simple and convenient manner.

More about "Phenols"

Phenols, a class of organic compounds featuring a hydroxyl (-OH) group attached to an aromatic ring, are widely distributed in nature and possess diverse biological and industrial applications.
These aromatic hydroxy compounds exhibit a range of chemical and physical properties, including antimicrobial, antioxidant, and pollution-reducing activities, making them a topic of significant research interest.
Phenolic compounds are studied across various fields, including pharmacology, environmental science, and material science.
Researchers exploring phenols may leverage tools like the TRIzol reagent, TRIzol, Agilent 2100 Bioanalyzer, RNeasy Mini Kit, HiSeq 2000, NanoDrop, HiSeq 2500, 2100 Bioanalyzer, and NanoDrop 2000 spectrophotometer to analyze their structure, function, and applications.
PubCompare.ai, an AI-driven platform, can optimize the phenols research workflow by helping researchers locate the best published, preprint, and patent procedures, while enhancing reproducibility and accuracy.
By utilizing this unique platform, scientists can elevate their phenols studies and drive innovation in this important area of research.
Synonyms for phenols include hydroxy-benzenes, phenolic compounds, and aromatic alcohols.
Related terms include polyphenols, flavonoids, and tannins.
The abbreviation 'Ph-OH' may also be used to refer to the phenol functional group.
Key subtopics in phenols research include biosynthesis, environmental fate, toxicology, and industrial applications.
Whether you're studying the antimicrobial properties of phenols, exploring their role in environmental remediation, or investigating their potential in material science, PubCompare.ai can be a valuable tool to enhance your research workflow and drive your phenols-related discoveries forward.