Formaldehyde

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Formaldehyde is a chemical compound with the formula CH2O. It is a colorless, flammable gas with a pungent odor. Formaldehyde is used as a chemical building block in the production of various products, including resins, adhesives, and disinfectants.

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Lab products found in correlation

Triton x 100, by Merck Group (151 mentions) Crystal violet, by Merck Group (109 mentions) Bovine serum albumin (bsa), by Merck Group (77 mentions) Ethanol, by Merck Group (67 mentions) Glutaraldehyde, by Merck Group (64 mentions) 4 6 diamidino 2 phenylindole (dapi), by Merck Group (62 mentions) Methanol, by Merck Group (53 mentions) Hoechst 33342, by Thermo Fisher Scientific (52 mentions) 4 6 diamidino 2 phenylindole (dapi), by Thermo Fisher Scientific (45 mentions) Dimethyl sulfoxide (dmso), by Merck Group (43 mentions) Phosphate buffered saline (pbs), by Merck Group (36 mentions) Fetal bovine serum (fbs), by Thermo Fisher Scientific (36 mentions) Acetic acid, by Merck Group (35 mentions) Hydrochloric acid (hcl), by Merck Group (34 mentions) Sodium chloride (nacl), by Merck Group (33 mentions) Phosphate buffered saline (pbs), by Thermo Fisher Scientific (32 mentions) Glycine, by Merck Group (30 mentions) Acetone, by Merck Group (29 mentions) Sodium hydroxide (naoh), by Merck Group (29 mentions) Glacial acetic acid, by Merck Group (23 mentions)

1 865 protocols using formaldehyde

Synchronizing Yeast Cell Cycle Stages

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G1 elutriation. G1 daughter cells were recovered from exponentially-growing cultures through elutriation - a physical method of cell cycle synchronization, used to separate cells according to their density and sedimentation velocity. For a detailed protocol see Lazar-Stefanita et al.²¹ (link) After elutriation, ∼1.5 × 10⁹ G1 cells were suspended in 150 mL fresh YPD at 30°C for 30 min and then crosslinked with 3% formaldehyde (Sigma-Aldrich) for Hi-C library preparation (see below).
Nocodazole. Metaphase cells were chemically synchronized using the microtubule disrupting drug, Nocodazole (Sigma-Aldrich). Exponentially-growing cultures (7 × 10⁶ cells/mL) were grown for 3 h at 30°C in YPD supplemented with 15 μg/mL Nocodazole. Cells were then crosslinked with 3% formaldehyde (Sigma-Aldrich) for Hi-C library preparation.
M phase ts mutants. Anaphase-synchronized cells were obtained through the thermosensitive (ts) mutant, cdc15-2.⁶⁰ (link) Exponentially-growing cultures (∼7 × 10⁶ cells/mL) of strains, carrying the mutated cdc15-2 allele, were transferred from the permissive temperature (25°C) to the non-permissive growing temperature (37°C). Cultures were incubated for 3 h at 37°C before being crosslinked with 3% formaldehyde (Sigma-Aldrich) for Hi-C library preparation (see below).

Lazar-Stefanita L., Luo J., Montagne R., Thierry A., Sun X., Mercy G., Mozziconacci J., Koszul R, & Boeke J.D. (2022). Karyotype engineering reveals spatio-temporal control of replication firing and gene contacts. Cell Genomics, 2(8), 100163.

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Quantification of Viral Plaque Formation

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Vero (ZIKV) or LLC-MK₂ (DENV and JEV) cells were cultured in 6-well cell culture plates at 37 ^ºC with 5% CO₂ for 22–24 h to obtain approximately 90% confluency. Before infection, cell culture supernatant (control) or stock virus were 10-fold serially diluted with BA-1 virus diluent (1× medium 199/Earle’s balanced salts, 0.05 M Tris-HCl [pH 7.6], 1% bovine serum albumin fraction V, 0.075% NaHCO3, 100 U of penicillin-streptomycin per ml). Cells were infected with 200 µl of the diluted cell culture supernatant or diluted virus at 37 ^ºC for 2 h with gentle rocking every 10 min. After that, the infected cells were overlaid with 4 ml of overlay medium (1.2% methylcellulose (Merck KGaA, Darmstadt, Germany) in DMEM supplemented with 2% FBS for ZIKV, or 4 ml of 0.8% Seakem LE agarose (Cambrex Bio Science Walkersville, Inc., Walkersville MD) in 1X nutrient solution for DENV 2 and JEV). The infected cells were incubated for a further 7 days at 37 ^ºC with 5% CO₂. On day 7, the overlay medium was removed and infected cells were then fixed with 1 ml of 3.7% formaldehyde (Merck KGaA, Darmstadt, Germany) in PBS for at least an hour at room temperature. After that, the formaldehyde was removed and the cells were washed with water prior to staining cells with 1% crystal violet (Merck KGaA, Darmstadt, Germany) in 20% ethanol. All samples were assayed in duplicate.

Sawadpongpan S., Jaratsittisin J., Hitakarun A., Roytrakul S., Wikan N, & Smith D.R. (2023). Investigation of the activity of baicalein towards Zika virus. BMC Complementary Medicine and Therapies, 23, 143.

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Perfusion and Cryosectioning of Mouse Brain

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Preparation and staining of mouse brain sections were previously described in [56 (link)]. In brief, the mice were deeply anesthetized with 10 : 1 mixture of ketamine 50 mg/ml (Tekam) and xylazine 20 mg/ml (Seton) (dose 0.1 ml/10 gm i.p.) diluted in 1X phosphate-buffered saline (PBS, pH = 7.4) (1X PBS) and then briefly perfused intracardially (flow rate: 8-10 ml/min for 2-5 min) with 1X PBS. This was followed by 10 min of 4% paraformaldehyde freshly prepared (Sigma-Aldrich) or commercially available 4% formaldehyde (a dilution of 37% formaldehyde solution, Sigma-Aldrich, in 1X PBS); all solutions were adjusted to pH 7.4. To ensure complete tissue fixation, brains were removed carefully and postfixed into the same fixative for 1 h at 4°C and then cryopreserved in 20-30% sucrose/PBS at 4°C in preparation for sectioning. Brains were then embedded in OCT compound (Tissue-Tek®, Ted Pella, Inc.) and sectioned sagittally into 14-20 μm thick slices at -20°C using a Leica CM3050 S cryostat (Leica Microsystems). They were then mounted on glass slides (Fisher Scientific) and stored at -80°C for further use in cresyl and immunofluorescence studies. The second group of brains was gently dissected to isolate the frontal cortex according to the mouse brain atlas [57 ], and the samples were stored at -80°C for a Western blotting assay.

Alshammari M.A., Khan M.R., Alasmari F., Alshehri A.O., Ali R., Boudjelal M., Alhosaini K.A., Niazy A.A, & Alshammari T.K. (2019). Changes in the Fluorescence Tracking of NaV1.6 Protein Expression in a BTBR T+Itpr3tf/J Autistic Mouse Model. Neural Plasticity, 2019, 4893103.

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Oil Red O Staining for Lipid Droplets

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The influence of LEAO, REAO, and SEAO on lipid droplet generating in 3T3-L1 cells was investigated using the Oil Red O Staining Protocol, after full differentiation (at day 8). Cells were washed with phosphate buffered saline (PBS) (Biosesang, Korea) and fixed with 4% Formaldehyde (Junsei Chemical Co., Ltd., Japan) for 5 min. Formaldehyde was removed and cells were rinsed with 60% isopropanol (Sigma-Aldrich Inc.). Cells were fixed with 4% Formaldehyde once again for 1 h and stained with 3.5 g/l of Oil Red O (Sigma-Aldrich Inc.) in 60% isopropanol for 10 min. The stained cells were washed with distilled water and entirely dried. The stained lipid droplets in cells were visualized by using a phase contrast microscope. Furthermore, stained dye was eluted by using 100% isopropanol and the absorbance was measured at 450 nm with a microplate reader (Molecular Devices).

Kim E.J., Kang M.J., Seo Y.B., Nam S.W, & Kim G.D. (2018). Acer okamotoanum Nakai Leaf Extract Inhibits Adipogenesis Via Suppressing Expression of PPAR γ and C/EBP α in 3T3-L1 Cells. Journal of microbiology and biotechnology, 28(10).

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Senescence-Associated β-Galactosidase Assay

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The 6-well plate cells were incubated with different treatments and washed three times with phosphate buffered saline (PBS), immobilized at room temperature with 4% formaldehyde (EMD Millipore, Billerica, MA, USA) for 10 min, washed three times with PBS, cultured cells were incubated at 37°C with SPiDER-Gal (Dojin) for 30 min, and finally the cells were observed under a microscope (Japan OLYMPUS Corporation). (Doura et al., 2016 (link))
Rat heart tissue specimen sections (6 µm) were likewise taken, fixed at room temperature with 4% formaldehyde (EMD Millipore, Billerica, MA, USA) for 10 min, washed three times with PBS, incubated overnight in SA-Gal staining solution, and aging changes were observed using a microscope.

Li Y., Liu M., Song X., Zheng X., Yi J., Liu D., Wang S., Chu C, & Yang J. (2020). Exogenous Hydrogen Sulfide Ameliorates Diabetic Myocardial Fibrosis by Inhibiting Cell Aging Through SIRT6/AMPK Autophagy. Frontiers in Pharmacology, 11, 1150.

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Quantifying Microtubule Cytoskeleton Organization

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Cells were fixed with 3.7% formaldehyde (Sigma) in PBS for 10 min at RT, followed by PBS washing 2× for 5 min. For microtubule staining, cells were fixed with 2.5% formaldehyde and 0.15% glutaraldehyde in PBS for 10 min at RT followed by quenching with 0.5 mg/ml sodium borohydride (Sigma) in PBS for 5 min 3×. Blocking and antibody staining was done in 1% BSA in PBS. Rabbit polyclonal ant-pericentrin antibody (Abcam) was used to stain for the MTOC at 1:1000 dilution, anti-myosin IIA antibody (Sigma) was used at 1:100, anti-myosin IIB antibody (Cell Signaling) was used at 1:150, anti-α-tubulin (Sigma) at 1:2000 and all primary antibodies were incubated at RT for 1 hour or overnight at 4°C. All secondary antibodies (Alexa dyes 488, 564, 647) were used in staining for 1 hour at RT at 1:300 dilution. TRITC-phalloidin (Sigma) was used with the donkey secondary antibodies at a concentration of 100 ng/ml and Hoechst 33342 (Invitrogen) was used to stain DNA at a concentration of 1 µg/ml for 10 min at RT. Imaging for quantification of MII levels and localization was performed using an inverted microscope (IX-71, Olympus) with a 40× LUCPlanFLN objective (NA 0.60) and a Cascade CCD camera (Photometrics). Image acquisition was performed with Image Pro software (Media Cybernetics, Inc.) and subsequently background was subtracted and image analysis was done using ImageJ.

Raab M, & Discher D.E. (2017). Matrix rigidity regulates the microtubule network polarization in migration. Cytoskeleton (Hoboken, N.J.), 74(3), 114-124.

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Investigating Menthol and Formaldehyde Effects on Neurons

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After allowing the neurites to freely extend for 48 hours, the DRG neurons were pretreated with capsazepine (a TRPV1 antagonist, 10 μM) (Sigma-Aldrich) for 30 minutes. Thereafter, the neurons were treated and cultured for 24 hours as follows: (1) formaldehyde group (n = 5), DRG neurons were exposed to formaldehyde (Sigma-Aldrich) 10 μM; (2) menthol group (n = 5), DRG neurons were exposed to menthol (Sigma-Aldrich) 300 μM; (3) PD98059 + formaldehyde group (n = 5), PD98059 (an ERK1/2 inhibitor, 10 μM) (Cell Signaling Technology, Danvers, MA, USA) was added 30 minutes before formaldehyde (10 μM) exposure; (4) PD98059 + menthol group (n = 5), PD98059 (10 μM) was added 30 minutes prior to menthol (300 μM) exposure; (5) control group (n = 5), DRG neurons treated only with the TRPV1 receptor antagonist capsazepine (10 μM). Because TRPA1 and TRPV1 channels interact in neurons (Ruparel et al., 2011), capsazepine, a TRPV1 antagonist, was used to block the effects of TRPV1.

Wang X.L., Cui L.W., Liu Z., Gao Y.M., Wang S., Li H., Liu H.X, & Yu L.J. (2019). Effects of TRPA1 activation and inhibition on TRPA1 and CGRP expression in dorsal root ganglion neurons. Neural Regeneration Research, 14(1), 140-148.

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Formaldehyde Inactivation of Infected Cells

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The formaldehyde (FA) inactivation solution was prepared from a 37% stock of formaldehyde (Sigma-Aldrich, Buchs, Switzerland, Cat. No. 33220) diluted 1:10 in PBS (Sigma, D8537), leading to the final FA concentration of 3.7% added to the infected cells (without media) in the inactivation protocol.

Seeburg U., Urda L., Otte F., Lett M.J., Caimi S., Mittelholzer C, & Klimkait T. (2023). Virus Inactivation by Formaldehyde and Common Lysis Buffers. Viruses, 15(8), 1693.

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ChIP-seq protocol for H3K4me3 and PRDM9 in mammalian cells

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H3K4me3 ChIP-seq from mouse spermatocytes was performed as previously described [9 (link)]. ChIP from HEK293 cell cultures were performed with modifications. After transfection cells were allowed to grow for 48 hours. For H3K4me3 ChIP cells were crosslinked by adding formaldehyde (SIGMA) to a final concentration of 1%, and incubated for 10 minutes. For FLAG-tagged PRDM9 ChIP, cells were crosslinked using freshly prepared paraformaldehyde added to a final concentration of 1% and incubated for 5 minutes. Excess formaldehyde was quenched by adding glycine to a final concentration of 125 mM. The medium was removed and the cells were washed once with phosphate-buffered saline (PBS, SIGMA). The PBS was removed and 2 ml of fresh PBS was added supplemented with protease inhibitor cocktail (SIGMA). The cells were collected by scrapping into a 2-ml Eppendorf tube and pelleted by centrifugation at 5000 x g at 4°C for 5 minutes. The PBS was removed and the cell pellet frozen in liquid nitrogen and stored at -80°C. For H3K4me3 ChIP chromatin isolation, MNase digestion, and immunoprecipitation steps were carried out as previously described for spermatocytes. For FLAG ChIP, chromatin was sheared using sonication and immunoprecipitation performed as described for mouse PRDM9 [30 (link)].

Baker C.L., Petkova P., Walker M., Flachs P., Mihola O., Trachtulec Z., Petkov P.M, & Paigen K. (2015). Multimer Formation Explains Allelic Suppression of PRDM9 Recombination Hotspots. PLoS Genetics, 11(9), e1005512.

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Cell Proliferation Assay via Crystal Violet

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Cells were reseeded in 12-well plates at a concentration of 15,000 cells per well, with 4 replicates of each condition. After removing the media and washing with PBS, we fixed the cells in 4% formaldehyde (Sigma-Aldrich, St. Louis, MO) and gently rocked them for 10 minutes at room temperature. The formaldehyde was then removed, and the cells were washed twice with PBS, incubated with 1% crystal violet (Sigma-Aldrich) while gently rocking for 10 minutes at room temperature, and then rinsed with water until the water washed clear, after which 0.1% SDS was added and incubated for 10 minutes while gently rocking. The absorbance of each well was then measured at 590 nm by using a SpectraMax M5 (Molecular Devices). crystal violet staining was performed on the same day as the initial cell seeding (day 0) and daily thereafter for 3–4 days. crystal violet absorbance readings measured on days 1–4 were normalized to that measured on day 0.

Tenga A., Beard J.A., Takwi A., Wang Y.M, & Chen T. (2016). Regulation of Nuclear Receptor Nur77 by miR-124. PLoS ONE, 11(2), e0148433.

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