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9 protocols using β galactosidase

1

Validating miR-149-3p Regulation of Prdm16 in HEK293T Cells

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Plasmids carrying the Renila luciferase gene linked to a fragment of the Prdm16
3′UTR harbouring miR-149-3p putative binding sites were co-transfected
into HEK293T cells (Human Embryonic Kidney, purchased from the Type Culture
Collection of the Chinese Academy of Sciences, Shanghai, China, authenticated by
STR Profiling, no mycoplasma contamination) along with control miRNA or
miR-149-3p mimic (Genepharm, Suzhou, China). A mutant 3′-UTR of Prdm16 was
constructed by mutagenesis of miR-149-3p from AGGGAGG into
GGAGGGA. HEK 293T cells were cultured in DMEM (Gibco,
Carlsbad, CA, USA) containing 10% FBS and seeded in 12-well plates. At
24 h after plating, 0.2 μg of firefly luciferase reporter
plasmid, 0.2 μg of β-galactosidase (cat# 10586-014)
expression vector (Ambion, Carlsbad, CA, USA), and equal amounts
(20 pmol) of miR-149-3p mimic or scrambled negative control RNA were
transfected into cells with Lipofectamine 2000 (cat# 11668-019) (Invitrogen,
Carlsbad, CA, USA) according to manufacturer's instructions. A
β-galactosidase vector was used as a transfection control. At 24 h
post-transfection, the cells were analysed using a luciferase assay kit
(cat# E4550) (Promega, Madison, WI, USA). All Experiments were performed in
triplicate wells for each condition and repeated five times independently.
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2

Luciferase reporter assay for miR-125b-5p and CREB1

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A luciferase reporter assay was performed to check if miR-125b-5p could bind to CREB1. Sequences binding to miR-125b-5p on CREB1 3'UTR were deleted to obtain the mutant. The CREB1 3′UTR wild-type and mutant sequences were inserted into the p-MIR-reporter (Ambion, Austin). The wild-types and mutant sequences were confirmed by sequencing. Subsequently, in 24-well plates, the 293T cells were seeded. At 70% confluency, the same amount of β-galactosidase (Ambion) and luciferase firefly reporter plasmids were transfected, with an equal amount of miR-125b-5p mimic/control mimic. Following a previously reported protocol, we performed luciferase assays [18 (link)].
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3

Measuring YAP Transcriptional Activity

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Luciferase reporter assay was performed to measure YAP transcriptional activity via detecting the luciferase activity of 8xGTIIC-luciferase plasmid, which is a YAP-responsive synthetic promoter driving luciferase expression plasmid. Briefly, 8xGTIIC-luciferase plasmid was co-transfected into HCC cells with β-Galactosidase (Ambion, Thermo Fisher Scientific) plasmid using Lipofectamine™ 2000 followed for 72 hours. After that, the luciferase activity of 8xGTIIC-luciferase plasmid was measured using a Luciferase Reporter Assay Kit (Cat # K801-200; BioVision, Inc., Milpitas, CA, USA). β-gal activity was determined using a β-Galactosidase Enzyme Assay System with Reporter Lysis Buffer (Cat # E2000; Promega Corporation, WI, USA) following the manufacturer’s protocols, which was used as a normalization control for luciferase activity.
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4

Protein Electrophoresis Analysis Using SDS-PAGE

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For the electrophoretic assay, proteins from the analyzed preparations were sedimented with trichloroacetic acid at a final concentration of 10% or were used without sedimentation in the case of their subsequent staining with zinc67 (link). Protein residues were analyzed by electrophoresis68 (link) with 0.1% SDS in 12.5% PAG. Electrophoresis in stacking gel was run at 90 V; in separating gel, at 180 V. Protein bands in gels were revealed by staining with a solution of Coomassie Brilliant Blue R-250 (Serva, Germany) and imidazole–ZnCl2 solutions. As molecular weight markers, we used SM0431 (Thermo Fisher Scientific, USA): β-galactosidase (116 kDa), bovine serum albumin (66.2 kDa), ovalbumin (45 kDa), lactate dehydrogenase (35 kDa), restrictase Bsp981 (25 kDa), β-lactoglobulin (18.4 kDa) and lysozyme (14.4 kDa).
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5

Quantifying Enzymatic Activity of β-Galactosidase

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β-galactosidase produces 5-bromo-4-chloro-3-indole (blue) from colorless 5-bromo-4-chloro-3-indole-beta-d-galactoglycosidese (X-gal). 109 phage particles immobilized with β-galactosidase or 109 HocSoc phage particles were added to a reaction tube and mixed with 1 μg X-gal (iScience, Yugong Biolabs, Inc.). After incubation for 30 min at 37 °C, color change of the reaction mixture was observed and recorded. Activity of β-galactosidase was quantified using o-nitrophenyl-β-galactoside (ONPG) as the substrate. The 200 μl reaction mixture containing 625 μM ONPG, 100 mM phosphate buffer, pH 6.8, 1 mM MgCl2, and various amounts of phage particles immobilized with β-galactosidase was incubated at 37 °C in a microplate spectrophotometer (Multiskan GO, Thermo Scientific Inc.). Absorbance of OD420 was read with 2-min intervals. Every reaction was performed in 3 parallel wells. Commercial β-galactosidase (Sigma-Aldrich, St. Louis, MO, USA) was used as the control.
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6

SDS-PAGE Analysis of Protein Supernatant

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The protein composition of the supernatant was determined using sodium dodecyl sulfate‐polyacrylamide gel electrophoresis (SDS‐PAGE) technique under native (no β‐mercaptoethanol) and reducing (with β‐mercaptoethanol) conditions in a modified Laemmli system (Laemmli, 1970) with 5% acrylamide in the stacking gel and 12% acrylamide in the separating gel. Protein bands were visualized by staining with Coomassie R250 brilliant blue. Standard proteins (Thermo Scientific, Shanghai, China) were used for molecular mass determination as follows: β‐galactosidase (116 kDa), bovine serum albumin (66.2 kDa), ovalbumin (45 kDa), lactate dehydrogenase (35 kDa), REase Bsp981 (25 kDa), β‐lactoglobulin (18.4 kDa), and lysozyme (14.4 kDa). After staining and destaining, the gels were scanned using a Bio‐Rad Gel Doc XR system and analyzed with Quantity One software.
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7

SDS-PAGE Protein Separation and Visualization

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The electrophoresis was performed in 12.5% PAG in the presence of sodium dodecyl sulfate according to the Laemmli method [57 (link)]. The samples were heated in a sample buffer (0.025 M Tris-HCl, 2% SDS, 10% glycerol, 0.7 M mercaptoethanol, bromophenol blue, pH 6.8) at 99 °C for 10 min. As markers, a mixture of protein standards (Thermo Fisher Scientific, Waltham, MA, USA) was used: β-galactosidase, 116.0 kDa; BSA, 66.2 kDa; ovalbumin, 45.0 kDa; lactate dehydrogenase, 35.0 kDa; REase Bsp981, 25.0 kDa; β-lactoglobulin, 18.4 kDa; lysozyme, 14.4 kDa. The electrophoresis in the concentrating gel was performed at 90 V; in the separating gel, it was performed at 180 V. Protein bands in the gel were revealed by staining with imidazole and ZnCl2 solutions [58 (link)].
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8

PLA2G3 Promoter Luciferase Assay

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A PLA2G3 promoter-luciferase construct was obtained from Switchgear Genomics (Menlo Park, CA; s707075). Derivatives harboring a triple point mutation in the first SRE-binding site of the promoter (CACCCCAT → CACCGATT) or a deletion of the first SRE-binding site (Smith et al., 1990 (link)) were generated using the QuikChange Site Directed Mutagenesis Kit (Stratagene, La Jolla, CA). HEK-293 cells were cotransfected with the appropriate promoter construct (100 ng), an expression construct encoding SREBP-1c (pIRES-SREBP1c), or control plasmid (pIRES-NEO; 10 ng) and β-galactosidase expression plasmid (Stratagene; 10 ng) using FuGENE HD Transfection Reagent (Roche, Basel, Switzerland). At 24 h posttransfection, whole-cell lysates were analyzed using a firefly luciferase assay system (Promega) and normalized for β-galactosidase (Applied Biosystems).
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9

Regulation of CRE-Luciferase Activity

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TLR-3 cells were plated in collagen-coated 24-well plates and transfected with 200 ng cAMP reponse element-luciferase (CRE-luciferase) reporter (Qiagen, Valencia, CA), 150 ng β-galactosidase, 200 ng mouse LRH-1, and 200 ng ATF2 (Addgene). 48 hr later, the cells were treated with TM or the following kinase inhibitors: 10 μM D-JNKi for JNKs (Sigma), 1 μM SB202190 for p38 (Tocris), 10 μM GW84362X for PLK1/PKL3 (Tocris, Bristol, UK), or 1 μM GSK650394A for SGK (Tocris). 24 hr after treatment, cells were lysed in Tropix lysis buffer (100 mM potassium phosphate, 0.2% TritonX-100, pH 7.8) plus DTT. Lysates were plated in triplicates in 96-well plates and 85 μl of reaction buffer was automatically injected by the luminometer. Reaction buffer for each well was prepared as follows: 0.7 μl galacton (Applied Biosystems, Foster City, CA), 88 μM luciferin, 2.4 mM ATP, and 11.9 mM MgCl2 in 0.11M Tris-phosphate buffer, pH 7.8. Firefly luciferase activity was measured and samples were incubated 1 hr at room temperature. 100 μl Tropix Accelerator (Applied Biosystems) was then automatically injected and measured to quantify β-galactosidase activity, which was used to normalize luciferase activity values.
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