Paraffin embedded mammary gland tissue sections were dewaxed using Xylene (Merck Millipore, Darmstadt, Germany; Cat#108298) for 3 × 5 min, and rehydrated in gradual dilutions of ethanol for 3 min each (2 × 100%, 1 × 90%, 1 × 70% and 1 × 50%), followed by 2 min in MilliQ water. Tissue sections were stained in haematoxylin (Sigma-Aldrich; Cat#HHS16) for 30 s, then stained in eosin (Sigma-Aldrich; Cat#318906) for 10 s. Sections were then dehydrated through gradual increase of ethanol concentration (2 min 90%, 2 × 1 min 100%), and cleared by 2 × 5 min in Xylene. Slides were then mounted with coverslips using Entellan mounting media.
Xylene
Manufactured by Merck Group
Sourced in United States, Germany, United Kingdom, India, Australia, Switzerland, China, Brazil, Sao Tome and Principe, France, Ireland, Italy, Macao, Poland, Malaysia, Portugal
Xylene is a common laboratory solvent used for various applications in scientific research and analysis. It is a clear, colorless liquid with a distinctive aromatic odor. Xylene's primary function is as a dehydrating agent and clearing agent in histological and microscopy sample preparation, where it is used to replace water and prepare samples for embedding in paraffin or resin.
Automatically generated - may contain errors
Lab products found in correlation
Ethanol, by Merck Group (68 mentions)
Hematoxylin, by Merck Group (26 mentions)
Toluene, by Merck Group (24 mentions)
Methanol, by Merck Group (21 mentions)
Paraformaldehyde (pfa), by Merck Group (21 mentions)
Chloroform, by Merck Group (15 mentions)
Sodium hydroxide (naoh), by Merck Group (15 mentions)
Formalin, by Merck Group (13 mentions)
Sodium chloride (nacl), by Merck Group (13 mentions)
Acetone, by Merck Group (12 mentions)
Dibutylphthalate polystyrene xylene (dpx), by Merck Group (12 mentions)
Dimethyl sulfoxide (dmso), by Merck Group (11 mentions)
Hydrogen peroxide, by Merck Group (10 mentions)
Paraffin wax, by Merck Group (10 mentions)
Acetic acid, by Merck Group (10 mentions)
Hematoxylin and eosin, by Merck Group (9 mentions)
Triton x 100, by Merck Group (9 mentions)
Hydrochloric acid (hcl), by Merck Group (9 mentions)
Dichloromethane, by Merck Group (8 mentions)
Permount, by Thermo Fisher Scientific (8 mentions)
426 protocols using xylene
1
Paraffin-Embedded Mammary Gland Tissue Staining
2
Histological Analysis of Testicular Tissue
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Sections were fixed in Bouin’s fluid, dehydrated in graded dilutions of ethanols (70–100%) and embedded in paraffin. For staining, 3 μm sections were cut and mounted on Superfrost Plus slides (Thermo Scientific, Dublin, Ireland). Cryosections were prepared as follows: testicular tissue samples (1 cm) were snap-frozen in liquid nitrogen immediately after removal. After cryotomy, sections (8 μm) were put on coated slides (Superfrost Plus, Menzel, Braunschweig, Germany) and dried at room temperature. The slides were frozen at −20 °C until use.
hematoxylin and Eosin (H&E) staining was carried out to investigate testicular morphology. Following dewaxing in xylene (Sigma-Aldrich, Wicklow, Ireland; room temperature [RT], 3 × 10 minutes [min]), rehydration in descending alcohols (RT, 100% 5 min, 100% 5 min, 80% 5 min, 70% 5 min) and distilled water (RT, 5 min), sections were put in hematoxylin (VWR, Dublin, Ireland; RT, 30 seconds [s]), running water (15 min), eosin (Sigma-Aldrich, Wicklow, Ireland; RT, 45 s) and then running water (5 min). Sections were then dehydrated in ascending alcohol solutions (RT, 70% 5 min, 80% 5 min, 100% 5 min, 100% 5 min), cleared in xylene (Sigma-Aldrich, Wicklow, Ireland; RT, 3 × 10 min), and mounted in DPX (Sigma-Aldrich, Wicklow, Ireland).
hematoxylin and Eosin (H&E) staining was carried out to investigate testicular morphology. Following dewaxing in xylene (Sigma-Aldrich, Wicklow, Ireland; room temperature [RT], 3 × 10 minutes [min]), rehydration in descending alcohols (RT, 100% 5 min, 100% 5 min, 80% 5 min, 70% 5 min) and distilled water (RT, 5 min), sections were put in hematoxylin (VWR, Dublin, Ireland; RT, 30 seconds [s]), running water (15 min), eosin (Sigma-Aldrich, Wicklow, Ireland; RT, 45 s) and then running water (5 min). Sections were then dehydrated in ascending alcohol solutions (RT, 70% 5 min, 80% 5 min, 100% 5 min, 100% 5 min), cleared in xylene (Sigma-Aldrich, Wicklow, Ireland; RT, 3 × 10 min), and mounted in DPX (Sigma-Aldrich, Wicklow, Ireland).
3
FFPE Sample Deparaffinization and DNA Extraction
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Ten-µm thickness of 4 sections of FFPE samples were deparaffinized by 2 steps of Xylene (Sigma-Aldrich Corp., St. Louis, Missouri, USA) for 5 minutes each, followed by centrifugation for 5 minutes at 1,6000 g (Microcentrifuge 5415D, Eppendorf, Germany). Xylene was cleared by 2 steps of absolute ethanol; by incubation for 5 minutes each step followed by centrifugation at 1,6000 g. ethanol (Sigma-Aldrich Corp., St. Louis, Missouri, USA) was evaporated by air drying in the chemical cabinet for 20-30 minutes. Genomic DNA from tumor tissues and corresponding control samples were prepared according to the manufacturer’s instructions Qiagen DNeasy kit (Qiagen GmbH, Hilden, Germany).
4
Histological Analysis of Spheroids and Organoids
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H&E staining was performed to evaluate the structure and composition of the spheroids and organoids. The procedure involved a 2-min deparaffinisation step with xylene (Sigma-Aldrich), followed by a rehydration step with graded ethanol solutions (100%, 90%, 80% and 70%) and tap water (each for 2 min). Next, samples were stained with Harris' haematoxylin (Sigma-Aldrich) for 5 min, followed by incubation with 0.5% acid alcohol for 2 sec, tap water for 2 min, 0.2% ammonia water (Sigma-Aldrich) for 20 sec and again tap water for 2 min. Samples were counter-stained with eosin (Sigma-Aldrich) for 3 min and dehydrated using graded ethanol solutions (70%, 80%, 90% and 100%; each for 10 sec), followed by a final clearing step with xylene for 2 min, before the slides were mounted using dibutylphthalate polystyrene xylene (DPX; Sigma-Aldrich).
5
H&E Staining of Ovary Sections
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H&E staining was performed according to a previously described method (3 (link)). Briefly, fresh tissues were immersed in 4% paraformaldehyde (Sigma-Aldrich) for 30 min at room temperature to allow fixation. Tissues were dehydrated using an ethanol gradient, embedded in paraffin, sectioned (thickness, 6 µm) and deparaffinized in xylene (Sigma-Aldrich). Tissue sections were stained with H&E (Sigma-Aldrich), cleared in xylene and mounted on slides using neutral balsam (Sigma-Aldrich). The number of atretic follicles was counted per microscope field, in three non-overlapping fields of ovary sections from each mouse.
6
Tissue Fixation and Histological Staining
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All fresh tissues were fixed for 30 minutes at room temperature in 4% paraformaldehyde (Sigma-Aldrich, St. Louis, MO, USA), followed by gradient ethanol dehydration, paraffin embedding, sectioning (with a thickness of 6 μm), and deparaffinization in xylene. The tissue sections were stained with haematoxylin-eosin (H & E, Sigma-Aldrich, St. Louis, MO, USA), clarified in xylene (Sigma-Aldrich, St. Louis, USA), and mounted in neutral resin (Sigma-Aldrich, St. Louis, MO, USA).
7
Assessing Exogenous Interference in DNA Analysis
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Assay performance characteristics were evaluated in the presence of each of the nine exogenous interfering substances when added to the DNA: i) deparaffinization solution (Qiagen Scientific) (1.69 Â 10 À4 mL/25 mL of eluate), ii) paraffin wax (in Xylene) (2.50 Â 10 À5 mL/25 mL of eluate), iii) Xylene (Sigma, St. Louis, MO) (2.50 Â 10 À5 mL/25 mL of eluate), iv) ethanol (Sigma) (1.69 Â 10 À4 mL/ 25 mL of eluate), v) proteinase K (Qiagen Scientific) (3.30 Â 10 À6 mL/25 mL of eluate), vi) wash solution (Norgen, ON, Canada) (6.25 Â 10 À1 mL/25 mL of eluate), vii) 1Â wash solution (Promega Corp., Fitchburg, WI) 6.25 Â 10 À1 mL/25 mL of eluate), viii) wash buffer AW1 (Qiagen Scientific) (6.25 Â 10 À2 mL/25 mL of eluate), and ix) wash buffer AW2 (Qiagen Scientific) (6.25 Â 10 À1 mL/ substance was added at the specified final concentration to extracted gDNA from 15 unique CRC FFPE tissue samples. Untreated samples were used as study controls. Mean mutation frequencies were also evaluated using a Dunnett test.
8
Rapid Immunofluorescent Staining for LCM
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In order to minimize RNA degradation and maintain quality of the tissue samples for laser capture microdissection we developed a rapid immunofluorescent staining protocol. OCT-embedded hypothalamus blocks were sectioned in a cryostat into 10 um thick sections and thaw-mounted onto glass slides. Sections were fixed in 75% ethanol for 30 s, then blocked and permeabilized with PBS containing 2% BSA (Sigma-Aldrich) for 30 s. Afterwards, sections were incubated with the primary antibody anti-NeuN 1:25 (Millipore®). PBS-washed slides were incubated in the dark for 3 min at room temperature with the secondary antibody Alexa-488 anti-mouse 1:50 diluted in PBS containing 2% BSA. The slides, again washed with PBS, subsequently underwent a standard dehydration process (75% ethanol, 30 s; 95% ethanol, 30 s; 100% ethanol, 30 s; 100% ethanol, 30 s), rinsed briefly in Xylenes (Sigma-Aldrich) for 1 min, and then transferred into another bath of fresh Xylenes for 5 min to further remove any trace of ethanol. Finally, the slides were air-dried for 5 min prior to laser capture microdissection.
9
Synthesis of Propargyl-Functionalized PEG
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Example 23
mPEG-OH+Br—CH2—CCH-mPEG-O—CH2—C≡CH
mPEG-OH with a molecular weight of 20,000 Da (mPEG-OH 20 kDa; 2.0 g, 0.1 mmol, Sunbio) was treated with NaH (12 mg, 0.5 mmol) in THF (35 mL). A solution of propargyl bromide, dissolved as an 80% weight solution in xylene (0.56 mL, 5 mmol, 50 equiv., Aldrich), and a catalytic amount of KI were then added to the solution and the resulting mixture was heated to reflux for 2 hours. Water (1 mL) was then added and the solvent was removed under vacuum. To the residue was added CH2Cl2 (25 mL) and the organic layer was separated, dried over anhydrous Na2SO4, and the volume was reduced to approximately 2 mL. This CH2Cl2 solution was added to diethyl ether (150 mL) drop-wise. The resulting precipitate was collected, washed with several portions of cold diethyl ether, and dried to afford propargyl-O-PEG.
10
Synthesis of Propargyl-Functionalized PEG
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Example 14
mPEG-OH+Br—CH2—C≡CH→mPEG-O—CH2—C≡CH
mPEG-OH with a molecular weight of 20,000 Da (mPEG-OH 20 kDa; 2.0 g, 0.1 mmol, Sunbio) was treated with NaH (12 mg, 0.5 mmol) in THF (35 mL). A solution of propargyl bromide, dissolved as an 80% weight solution in xylene (0.56 mL, 5 mmol, 50 equiv., Aldrich), and a catalytic amount of KI were then added to the solution and the resulting mixture was heated to reflux for 2 hours. Water (1 mL) was then added and the solvent was removed under vacuum. To the residue was added CH2Cl2 (25 mL) and the organic layer was separated, dried over anhydrous Na2SO4, and the volume was reduced to approximately 2 mL. This CH2Cl2 solution was added to diethyl ether (150 mL) drop-wise. The resulting precipitate was collected, washed with several portions of cold diethyl ether, and dried to afford propargyl-O-PEG.
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