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Safeclear is a laboratory equipment product designed for safe handling and storage of hazardous materials. The core function of Safeclear is to provide a secure and contained environment for working with dangerous substances.

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Lab products found in correlation

Avidin biotin blocking kit, by Thermo Fisher Scientific (2 mentions) Axiovert 200 microscope, by PerkinElmer (2 mentions) Openlab3, by PerkinElmer (2 mentions) Dolichos biflorus agglutinin dba, by Vector Laboratories (2 mentions) Prolong gold, by Thermo Fisher Scientific (2 mentions) Superfrost plus, by Thermo Fisher Scientific (2 mentions) Edgar degas eosin, by Biocare Medical (2 mentions) Cat hematoxylin, by Biocare Medical (2 mentions) Permount, by Thermo Fisher Scientific (2 mentions) Vectamount, by Vector Laboratories (1 mentions) Axioscope 2 microscope, by Zeiss (1 mentions) Vectashield, by Vector Laboratories (1 mentions) Retrievagen a, by BD (1 mentions) Bright field microscopy, by Keyence (1 mentions) A1r multiphoton microscope, by Nikon (1 mentions) Fluoroshield dapi, by Merck Group (1 mentions) Ihc antigen retrieval solution, by Thermo Fisher Scientific (1 mentions) Apoptag red in situ apoptosis detection kit, by Merck Group (1 mentions) A1r multiphoton confocal microscope, by Nikon (1 mentions) Biotin conjugated anti mouse secondary antibody, by Vector Laboratories (1 mentions)

15 protocols using safeclear

1

Immunohistochemical Analysis of Enteroid Structure

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Following collection, we embedded the enteroids in paraffin. Sections were 4uM. Slides were baked for 1hour at 65°C. The paraffin was removed by using Safe Clear (Fisher Scientific, MA). Antigen retrieval was achieved by application and steaming with eBioscience IHC Antigen Retrieval Solution. Thereafter, a cold PBS wash and blocking with 5% normal goat serum with 0.1% triton for 30 minutes was performed. The enteroids were then incubated overnight at 4°C with primary antibodies against claudin-1, claudin-2, claudin-3, claudin-4, occludin, E-cadherin or ZO-1. Subsequently slides were washed and incubated with a secondary antibody (1:1000 dilution) at room temperature for 1 hour. Slides were mounted with DAPI fluoroshield (Sigma, MO). All protocols were conducted according to the instructions. Fluorescent imaging was performed using the Nikon A1R multiphoton confocal microscope. Image analysis was performed using ImageJ.
Enteroid slides were treated according to the Apoptag Red In Situ apoptosis detection kit (MilliporeSigma, MA), using Safe Clear (Fisher Scientific, MA) to replace xylene washes. Slides were counterstained and mounted using DAPI fluoroshield (Sigma, St. Louis, MO). Apoptotic cells were visualized using the Nikon A1R Multiphoton microscope.
Buonpane C., Ares G., Yuan C., Schlegel C., Liebe H, & Hunter C. (2020). Experimental modeling of necrotizing enterocolitis in human infant intestinal enteroids. Journal of investigative surgery : the official journal of the Academy of Surgical Research, 35(1), 111-118.
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2

Paraffin Sections H&E Staining

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Paraffin sections for H&E staining were dewaxed with Safeclear (Fisher Scientific, Hampton, NH) and rehydrated with graded aqueous solutions of isopropanol. The sections were stained for 4 min with CAT Hematoxylin (Biocare Medical, Concord, CA), rinsed in running tap water for 30 sec followed by three quick dips in saturated lithium carbonate and a rinse in distilled water. This was followed by 90% ethanol for 2 min, Edgar Degas Eosin (Biocare Medical) for 2 min and 3 quick rinses in 100% ethanol. The sections were cleared with Safeclear (two 5 min incubations) and were mounted with Permount (Fisher Scientific).
Pearring J.N., San Agustin J.T., Lobanova E.S., Gabriel C.J., Lieu E.C., Monis W.J., Stuck M.W., Strittmatter L., Jaber S.M., Arshavsky V.Y, & Pazour G.J. (2017). Loss of Arf4 causes severe degeneration of the exocrine pancreas but not cystic kidney disease or retinal degeneration. PLoS Genetics, 13(4), e1006740.
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3

Paraffin Sections H&E Staining

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Paraffin sections for H&E staining were dewaxed with Safeclear (Fisher Scientific, Hampton, NH) and rehydrated with graded aqueous solutions of isopropanol. The sections were stained for 4 min with CAT Hematoxylin (Biocare Medical, Concord, CA), rinsed in running tap water for 30 sec followed by three quick dips in saturated lithium carbonate and a rinse in distilled water. This was followed by 90% ethanol for 2 min, Edgar Degas Eosin (Biocare Medical) for 2 min and 3 quick rinses in 100% ethanol. The sections were cleared with Safeclear (two 5 min incubations) and were mounted with Permount (Fisher Scientific).
Desai P.B., San Agustin J.T., Stuck M.W., Jonassen J.A., Bates C.M, & Pazour G.J. (2018). Ift25 Is Not a Cystic Kidney Disease Gene but Is Required for Early Steps of Kidney Development. Mechanisms of development, 151, 10-17.
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4

Immunohistochemical Analysis of Amygdala and Hippocampal Proteins

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Amygdala, hippocampal, and SMTG specimens were fixed in 10% formaldehyde, embedded in paraffin, and cut into ~8 μm thick sections. Slides were baked in a 40°C oven overnight, deparaffinized using SafeClear (Fisher Scientific), and rehydrated through a series of graded alcohols to water. Slides were boiled for 10 minutes in Borg Decloaker antigen retrieval solution, pH = 6.0 (Biocare Medical) before blocking endogenous peroxidase activity with 3% hydrogen peroxide + 10% methanol. The slides were blocked (0.1 M Tris buffer with 0.1% Triton X-100 and 2% bovine serum albumin) and incubated overnight at 4°C in the foll owing primary antibodies: 1:25 rabbit polyclonal anti-ΔCN; 1:500 mouse monoclonal anti-CN-Aα (C-terminus) (Sigma);. 1:50 mouse monoclonal anti-Aβ (Vector Laboratories. Secondary antibodies were added at a 1:200 dilution for 1 hour at room temperature as follows: anti-mouse IgG + horse normal serum or anti-rabbit IgG + goat normal serum. Following secondary antibody, signal was amplified with avidin-biotin complex for 1 hour at room temperature and then detected using either DAB or SG substrates (Vector Laboratories). Following dehydration through a series of graded alcohol and clearing (SafeClear), slides were permanently mounted using VectaMount (Vector Laboratories) and coverslipped.
Pleiss M.M., Sompol P., Kraner S.D., Abdul H.M., Furman J.L., Guttmann R.P., Wilcock D.M., Nelson P.T, & Norris C.M. (2016). Calcineurin proteolysis in astrocytes: Implications for impaired synaptic function. Biochimica et biophysica acta, 1862(9), 1521-1532.
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5

Age-Dependent Brain Vacuolization Analysis

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Flies of each genotype were aged to 20 days and heads were processed as previously described [19] (link), [20] (link). Briefly, heads were cut in 7 µm serial sections, the paraffin was removed in SafeClear (Fisher Scientific), sections were embedded in Permount, and analyzed with a Zeiss Axioscope 2 microscope using the auto-fluorescence caused by the eye pigment (no staining was used). Experimental and control flies were put next to each other in the same paraffin block, cut, and processed together. Microscopic pictures were taken at the same level of the brain, the vacuoles (identified by being unstained and exceeding 50 pixels in size) were counted and the vacuolized area was calculated using our established methods [19] (link), [20] (link).
Long D.M., Blake M.R., Dutta S., Holbrook S.D., Kotwica-Rolinska J., Kretzschmar D, & Giebultowicz J.M. (2014). Relationships between the Circadian System and Alzheimer's Disease-Like Symptoms in Drosophila. PLoS ONE, 9(8), e106068.
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6

Optimized Iron Histochemical Staining

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Sections were deparaffinized with SafeClear (Fisher Scientific, catalog number 23314629) (2 × 3 min), excess SafeClear tapped off, and then stained with 50% acetone/1% potassium ferrocyanide trihydrate (Millipore Sigma, catalog number P3289-100G)/0.05 N HCl (final concentrations) for 1 hr; followed by washes in H2O; 40 mg 3,3′-diaminobenzidine tetrahydrochloride (DAB) (Millipore Sigma, catalog number D5905) in 160 ml Tris buffered saline (Millipore Sigma, catalog number 94158-10TAB) with 640 µl 30% hydrogen peroxide for 30 min; H2O; upgraded alcohols; SafeClear; permanent mounting media.
Instead of the 70–80% acetone used by Hirose et al. (1970) , we observed that a 50% acetone concentration gave a suitable balance between allowing enough solubility of potassium ferrocyanide, the iron histochemical reagent, and the ability to achieve discrete staining. Furthermore, this concentration of acetone facilitated the wetting of the tissue section following the SafeClear step. Control slides were stained with 50% acetone/0.05 N HCl in place of the 50% acetone/1% potassium ferrocyanide trihydrate/0.05 N HCl solution.
LeVine S.M., Zhu H, & Tague S.E. (2021). A Simplified Method for the Histochemical Detection of Iron in Paraffin Sections: Intracellular Iron Deposits in Central Nervous System Tissue. ASN NEURO, 13, 1759091420982169.
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7

Immunofluorescence Analysis of Ovarian Aging

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IF was performed on paraffin-embedded sections from E56, P1, P5, P8, P15, P28, P90, P6MO, SUB 3 yr, EX-SUB 3 yr, SUB 6 yr, Queen 6 yr, and SUB 10 yr ovaries. Slides were deparaffinized and rehydrated with 3 washes of Safeclear (Fisher Scientific, Pittsburgh, PA. USA) for 10 minutes each, followed by 3 washes of each concentration in a graded series of ethanol (100%, 95%, 80%, 70%) for 5 minutes. After rinsing the slides 2 times for 5 minutes in distilled water, the slides were incubated in sodium citrate pH 6.0 during 40 min at 95 °C. Permeabilization was performed in 0.2% of Triton-X 100 in PBS for 1 h. Sections were blocked for 4 h in blocking solution (2.52 mg/ml glycine, 10% goat serum, 3% BSA, 0.2% Tween 20 in PBS) and then incubated with primary antibody (diluted in blocking solution) overnight at RT. After 2 washes of 10 min with 0.1% Tween 20 in PBS (PBS-Tw20), the slides were incubated with secondary antibodies for 2 hours at RT. The slides were rinsed twice with PBS-Tw20 for 5 min. Cell nuclei were counterstained with DAPI and mounted in Vectashield (Vector Laboratories, Burlingame, CA).
Brieño-Enríquez M.A., Faykoo-Martinez M., Goben M., Grenier J.K., McGrath A., Prado A.M., Sinopoli J., Wagner K., Walsh P.T., Lopa S.H., Laird D.J., Cohen P.E., Wilson M.D., Holmes M.M, & Place N.J. (2023). Postnatal oogenesis leads to an exceptionally large ovarian reserve in naked mole-rats. Nature Communications, 14, 670.
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8

Immunohistochemistry of Kidney Paraffin Sections

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7 µm kidney paraffin sections were cut and transferred to slides (Superfrost plus, Fisher Scientific). Sections were dewaxed (Safeclear, Fisher Scientific) and rehydrated with graded aqueous isopropanol. Antigen retrieval was carried out with 10 mM sodium citrate, pH 6 in an autoclave (250F for 40 min). Sections were blocked for 30 min (4% non-immune goat serum, 0.1% cold water fish skin gelatin, 0.1% Triton X-100, 0.1% Tween-20 in TBS). 1% BSA and 0.05% SDS were added to the blocking solution in the ANKS6 labeling experiments to reduce background. Incubation with primary antibodies/lectin was carried out overnight at 4C: T1α (1:1000, Developmental Studies Hybridoma Bank, University of Iowa), fluorescein-conjugated Dolichos biflorus agglutinin (DBA, 1:200, Vector Labs), anti-acetylated tubulin, anti-ANKS6 and secondary antibodies as above. For anti-ANKS6 IF, a biotin layer was employed to enhance labeling of ANKS6, requiring endogenous biotin to be blocked (Avidin/Biotin blocking kit, Life Technologies) prior to application of the biotin-conjugated secondary antibody (Fab fragment of goat anti-rabbit IgG at 1:250, Jackson Immunochemicals) and streptavidin-Alexa 488 at 1:400. Slides were incubated in DAPI and mounted with Prolong Gold (Life Technologies). Imaging was carried out using a Zeiss Axiovert 200 microscope and OpenLab 3.1.5 software (Improvision).
Czarnecki P.G., Gabriel G.C., Manning D.K., Sergeev M., Lemke K., Klena N.T., Liu X., Chen Y., Li Y., San Agustin J.T., Garnaas M.K., Francis R.J., Tobita K., Goessling W., Pazour G.J., Lo C.W., Beier D.R, & Shah J.V. (2015). ANKS6 is the critical activator of NEK8 kinase in embryonic situs determination and organ patterning. Nature communications, 6, 6023.
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9

Immunohistochemical Detection of EPS8 in Mouse Tumors

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Detection of EPS8 in mouse tumour sections was carried out as follows. Five-micrometre tissue sections were dewaxed in Safe-Clear (Fisher Scientific, Pittsburgh, PA) and rehydrated, and antigen retrieval was performed by incubation in Retrievagen A (BD Biosciences, CA) at 95 °C for 30 min. After cooling to ambient temperature, endogenous peroxidase was blocked by incubation in 3% hydrogen peroxide for 15 min; slides were washed in TBS pH 8.0 and then blocked using a commercially available kit (M.O.M. Immunodetection Kit—Peroxidase; Vector Laboratories, Burlingame, CA). Sections were then incubated with EPS8 antibody (12.5 μg/ml) or the equivalent concentration of normal mouse IgG as control at ambient temperature for 1 h, washed in TBS and then incubated sequentially with biotinylated secondary antibody and streptavidin peroxidase reagent, developed using 3, 3’-diaminobenzidine substrate, counterstained with haematoxylin, dehydrated, mounted and imaged by brightfield microscopy (Keyence Corporation, Itasca, IL).
Shahoumi L.A., Khodadadi H., Bensreti H., Baban B, & Yeudall W.A. (2020). EPS8 phosphorylation by Src modulates its oncogenic functions. British Journal of Cancer, 123(7), 1078-1088.
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10

Immunohistochemical Analysis of Matriptase in Murine Tissues

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Organs were collected from mice and fixed in 4% paraformaldehyde in PBS for 24 h, embedded into paraffin, and sectioned. Tissue sections were cleared with xylene-substitute (Safe Clear, Fisher Scientific), rehydrated in a graded series of alcohols, and boiled in Reduced pH Retrieval Buffer (Bethyl, Montgomery, TX) for 20 min for antigen retrieval. The sections were blocked for 1 h in PBS containing 10% horse serum and incubated at 4 °C overnight with sheep anti-human matriptase (catalogue no. AF3946, R&D Systems). The slides were washed three times in PBS and incubated at room temperature for 45 min with secondary antibodies, using Alexa Fluor 594-labeled donkey anti-sheep (Invitrogen) or a biotin-conjugated anti-mouse secondary antibody (1:1000, Vector Laboratories, Burlingame, CA) and a Vectastain ABC kit (Vector Laboratories) using 3,3-diaminobenzidine as the substrate (Sigma-Aldrich). The tissue sections were washed three times for 5 min with PBS and mounted with VectaShield Hard Set Mounting Medium (Vector Laboratories).
Friis S., Tadeo D., Le-Gall S.M., Jürgensen H.J., Sales K.U., Camerer E, & Bugge T.H. (2017). Matriptase zymogen supports epithelial development, homeostasis and regeneration. BMC Biology, 15, 46.
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