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11 protocols using ls004174

1

Isolation and Fractionation of Adipose Tissue

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iWAT and gWAT were excised and minced using a scalpel. Minced samples were placed in DMEM containing collagenase type 2 (LS004174; Worthington) at a final concentration of 2 mg/mL. Samples were incubated in an orbital shaker at 37 °C for 0.5 to 1 h. After digestion was completed, samples were passed through a sterile 70-µm cell strainer (352350; BD Biosciences) and diluted with DMEM to a final volume of 20 mL. The cell suspension was centrifuged at 200 × g and RT for 5 min. The upper fraction contained primary adipocytes, which were washed with PBS three times and used for further analysis. The lower fraction was centrifuged at 1,000 × g at RT for 5 min. The cell pellets were resuspended in 5 mL of red blood cell lysis buffer (158902; Qiagen), incubated for 3 min and RT, and then, washed three times using PBS. Cell pellets were collected as the SVF and used for further experiments.
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2

Isolation and Transfection of Adipocytes

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Subcutaneous fat tissue in the abdominal region of the body was collected under sterile conditions from patients with and without endometriosis. The tissue was subsequently minced into fine pieces (1–2 mm), and then digested in buffer containing collagenase type 2 (0.83 mg/ml, #LS004174, Worthington Biochemical Corporation, NJ) in sterile Hank’s balanced salt solution (HBSS, Life Technologies, CA, #14185–052) with 3% bovine serum albumin (BSA), calcium chloride (1.23 mM), magnesium chloride (1.03 mM) and zinc chloride (0.83 mM) for 75 min at 37 °C. The cell pellet was collected by centrifugation at 300×g for 3 min, re-suspended in HBSS with 3% BSA, and filtered through a sterile 40 μm (BD Biosciences CA, #352340) nylon mesh filter. The cells were then re-suspended in the growth medium DMEM/F12 medium (Life Technologies) containing 10% fetal bovine serum (FBS) and antibiotics (2% anti-anti), and plated and cultured in a T75 tissue culture flask that was maintained at 37 °C and 5% CO2-atmosphere. After 48 h, the non-adherent cells were washed off with phosphate buffered saline (PBS) while the adherent adipocytes were grown to 75% confluence. After the third passage the cells were transfected with miRNAs.
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3

Extraction of Newborn Rat Osteoblasts

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The calvariae of newborn rats were cut into chips and digested in a digestive solution of α-MEM medium containing 1% type 2 collagenase (LS004174, Worthington, OH, USA) and 0.05% trypsin for 30 min. After removing the solution, fresh digestive solution was added to digest the calvariae chips; this process was repeated three times. Finally, after the fourth time, centrifuged osteoblasts, and calvariae chips were cultured in α-MEM medium containing 10% FBS and 1% Antibiotic-Antimycotic Solution.
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4

Single-cell RNA-seq of NSCLC Pleural Effusions

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Samples were collected after receiving consent and approval from the Institutional Review Board (IRB No. 2010-04-039 and IRB No. 2019-05-049) at Samsung Medical Center. The collected pleural effusions of NSCLC patients were centrifuged at 1,500 rpm for 15 min, after which the samples were washed with PBS. Thereafter, samples were digested using mixtures of collagenase type Ⅱ (LS004174; Worthington Biochemical Corporation, Lakewood, NJ, USA) plus deoxyribonuclease Ⅰ (LS002139; Worthington Biochemical Corporation) for 15 min at 37°C. Afterward, digested cells were passed through a 40-μm pore filter and subjected to RBC lysis for 10 min at room temperature. After washing with PBS, cells on the plate were incubated for 15 min in a CO2 incubator. Only floating cells on the plate were collected, while adherent cells were excluded. The counted cells were then stocked and frozen. Except for one surgical sample, eight samples were thawed for library preparation and sequenced using 10x Chromium Single Cell Gene Expression Solution v2 (10x Genomics, Pleasanton, CA, USA) according to the manufacturer’s protocols. Six out of nine study patients were females, and additional clinical information for the patients are provided in Table S1.
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5

Isolation and culture of rat cardiomyocytes

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NCM and NCF were isolated from heart ventricles of one- to three-day old Wistar rats (Janvier Labs, Le Genest-Saint-Isle, France) as previously described [41 (link)]. Briefly, minced ventricular tissue was digested with type II collagenase (LS004174, Worthington, Lakewood, NJ, USA) and pancreatin (P3292, Sigma-Aldrich, St. Louis, MO, USA), and dissociated cells were pelleted by centrifugation at 800× g. NCMs were separated from NCFs via discontinuous Percoll gradient (bottom 58.5%, top 40.5% [v/v], P4937, Sigma-Aldrich, St. Louis, MO, USA) for 30 min at 1600× g. NCMs were seeded at 2.5 × 106 cells per 100 mm collagen-coated culture dish and were cultured in a 4:1 mixture of DMEM (D1152, Sigma Aldrich, St. Louis, MO, USA) and Medium 199 (M4530 Sigma-Aldrich, St. Louis, MO, USA), supplemented with 10% horse serum (HS) (16050122, Thermo Fisher Scientific, Waltham, MA, USA), 5% fetal calf serum (FCS) (30-2020, ATCC, Manassas, VA, USA), and 1% penicillin-streptomycin (PS) (15140-122, Gibco, Waltham, MA, USA) for 5 days at 37 °C under 5% CO2 atmosphere. NCFs were seeded at 2 × 106 cells per 100 mm culture dish and were cultured in DMEM (31966-02, Gibco, Waltham, MA, USA), 10% FCS, and 1% PS for 48 h at 37 °C under 5% CO2 atmosphere. NCF at passage 1 were used for experiments.
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6

Isolation and Characterization of Neonatal Cardiac Cells

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The study was designed in accordance with and approved by the institutional review committees at San Diego State University along with the institutional review board (#120686) and no informed consent was required. Neonatal cells were derived from nonsurgically obtained postmortem cardiac tissue. Cells were isolated as previously published.12 Briefly, heart samples were mechanically minced into 1‐mm3 pieces and digested in collagenase II (150 U mg/mL, Worthington, LS004174) followed by brief low‐speed (850 rpm for 2 minutes) centrifugation to remove cardiomyocytes and tissue debris. The supernatant was subjected to magnetic‐activated cell sorting using c‐kit–conjugated microbeads (Miltenyi Biotec, #130‐091‐332), and c‐kit–enriched cells were plated in human c‐kit CIC media. The c‐kit–negative population was further purified by magnetic‐activated cell sorting for MSC surface markers CD90 and CD105. c‐kit CICs and MSCs were incubated at 37°C in 5% CO2 and used for cellular fusion between passages 5 and 10. Media used in the study are listed in Table S1.
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7

Isolation and Analysis of Cardiac Side Population Cells

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CSPs were isolated as previously described [21 (link)]. The minced cardiac tissue from freshly isolated mouse hearts was digested using collagenase type 2 (LS004174, Worthington Biochemical Corp, Lakewood, NJ, USA) and dispase (17105–041, Life Technologies). The cells were resuspended at a density of 1.0 × 106/mL in PBS containing 3% fetal bovine serum. The cells were incubated in 1 μg/mL Hoechst 33342 dye (H3570, Molecular Probes) for 60 min at 37°C in the dark, with or without 50 μM verapamil. Following incubation, the cells were analyzed using Altra flow cytometric analysis (Beckman Coulter, Fullerton, CA, USA). Hoechst 33342 dye was excited at 350 nm using an ultraviolet laser. Fluorescent emission was detected using 450-nm bandpass (Hoechst blue) and 675-nm longpass (Hoechst red) filters, respectively. Isolated CSPs were used for in vitro incubation experiments or directly centrifuged onto slides using a CytoSpin Cytocentrifuge (Thermo Fisher Scientific, Waltham, MA, USA) at 71.8 × g for 5 min. For the β-galactosidase expression analysis, isolated CSPs and residual cardiomyocytes were fixed with 0.25% glutaraldehyde for 10 min and stained in X-gal staining solution for 1 h. For normal immunofluorescence staining, CSPs were fixed with 4% paraformaldehyde for 10 min and stained using the method described for fresh-frozen section staining.
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8

Extracellular Vesicles Isolation Protocol

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EVs were isolated by ultracentrifugation from HeLa conditioned culture media (media from 4 dishes/sample), human plasma (250 µL/sample) and human cardiac biopsies (200 mg/sample were minced and incubated in 6 mL PBS 1X containing 1 mg/mL type II collagenase (LS004174, Worthington) at 37 °C for 30 min with agitation). Conditioned culture media, plasma and cardiac minced tissue-containing PBS were centrifuged at 3000 g to remove debris and dead cells. The supernatants were ultracentrifuged at 20,000g (70 min, 4 °C) to pellet large EVs (lEVs), then at 100,000g (70 min, 4 °C) to pellet small EVs (sEVs). Rotors used were either Beckman 50.2 Ti or SW-32.1 (337,901/369651 Beckman Coulter France, Villepinte, France).
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9

Mouse VSMC Isolation and Culture

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Mouse VSMCs were derived from thoracic-abdominal aortas isolated from 3–4-week-old mice by removing the adventitia and endothelial layer using an enzyme mixture containing collagenase Type II (Worthington Biochemical, LS004174), soybean trypsin inhibitor (Worthington Biochemical, LS003570), and elastase (Worthington Biochemical, LS002279). They were maintained in DMEM/F12 media (Gibco, 11320) containing 20% FBS, L-glutamine, and P/S. Cells were used at passages under 10 for the experiments.
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10

Isolation of Coronary Perivascular Adipose Tissue

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Coronary PVAT was obtained from 4 patients undergoing heart transplantation and digested as described previously.28 (link) Briefly, coronary PVAT was collected in 10 mL DMEM (11885084; Gibco) containing 10% fetal bovine serum (10091148; Gibco) on ice. Samples were washed by PBS to remove the remaining blood cells and then cut into small pieces. These small pieces were washed by PBS again and digested in DPBS (14040133; Gibco) containing 0.1% (w/v) collagenase (LS004174; Worthington) at 37 °C for 60 minutes, followed by gently shaking. The cell suspension was centrifuged at 300g at 21 °C for 5 minutes. A vigorous shaking was performed for 10 s to ensure that individual cells are released from the strands of fibrous tissue. Then a second centrifugation (300g) was performed and supernatant was discarded, and the cell pellets were resuspended in 10 mL DMEM, followed by a third centrifugation (300g). Finally, the supernatant was discarded, and the cell pellets were resuspended in 10 mL fibroblast growth medium (C-23010; Sigma) containing 10% fetal bovine serum and 1% penicillin and streptomycin and culture in 5% CO2 at 37 °C. Early passage (P2 and P3) cultures were used for the cell migration assay and cell culture immunostaining.
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