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18 protocols using gapdh

1

HepG2 cell culture protocol

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HepG2 (human hepatocellular liver cell line) was obtained from the Korea Research Institute of Bioscience and Biotechnology (Daejeon, Korea) and grown in Eagle’s minimum essential medium (EMEM), supplemented with 10% fetal bovine serum and 100 U/mL penicillin/streptomycin sulfate. Cells were incubated in a humidified incubator at 37 °C in a 5% CO2 atmosphere. EMEM, penicillin, and streptomycin were purchased from HyClone Laboratories (Logan, UT, USA). Oligonucleotide primers for LDLR, PCSK9, and GAPDH were purchased from Bioneer Corp. (Daejeon, Korea). Berberine·HCl was purchased from Chengdu Biopurify Phytochemicals Ltd. (Sichuan, China).
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2

Integrin and TNFR Expression Analysis

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AGS cells (3 × 105 cells) were seeded in six-well plates. RNA was extracted from cells and isolated using Trizol reagent (Invitrogen, Carlsbad, CA, USA) in accordance with the Trizol protocol and cDNA was synthesized using TOP-script RT DryMIX (Enzynomics). RT-PCR was performed using 2× Hot TaqMasterMix (MGmed, Seoul, Korea). Primer pairs for integrin αV (P254519V), TNFRSF9 (P201215V), TNFSF10 (P144740V), TNFR1 (P253379V), TNFR2 (P199275V), VGLL1 (P227101V), TEAD4 (P130115V), and GAPDH (P267613V) were purchased from Bioneer. The sequences of RPL13A primer pair were as follows: (F) 5′-CATCGTGGCTAAACAGGTAC-3′, (R) 5′-GCACGACCTTGAGGGCAGC-3′.
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3

Cholesterol Biosynthesis Regulation Study

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Collagen (native Collagen fibrils (type I) from equine tendons) and ADP were purchased from Chrono-Log (Havertown, PA, USA). An ATP assay kit was purchased from Biomedical Research Service Centre (Buffalo, NY, USA), and TRIZOL solution was obtained from Invitrogen (Carlsbad, CA, USA). Primers against SREBP-2, ACAT-1, ACAT-2, HMG-CoA, and GAPDH were obtained from Bioneer (Daejeon, Republic of Korea). Primer sequences have been given in Table 1. Water was obtained from J. T. Baker (Phillipsburg, NJ, USA). All chemicals were of reagent grade.
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4

Comprehensive Cellular Evaluation Protocol

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RPMI-1640 medium, FBS, penicillin (100 U/mL), and streptomycin sulfate (100 (μg/mL) are from Life Technologies. The MTT, dimethyl sulfoxide (DMSO), RNase A, leupeptin, aprotinin, phenylmethylsulfonylfluoride (PMSF), dithiothreitol, and Triton X-100 were purchased from Sigma-Aldrich Co. CREB-binding protein (CBP), PTGS2, CFLAR, BCL2, BCL2L1, NF-κB p65 subunit, PARP, and β-actin antibodies were purchased from Santa Cruz Biotechnology, Inc. XIAP antibody was purchased from BD Biosciences. RSF1 and hSNF2H antibodies were purchased from Upstate. The RNA Extraction Kit was purchased from Intron Biotechnology. The Luciferase Assay Kit was purchased from Promega. pNF-κB–Luc reporter plasmid was purchased from BD Biosciences. Lipofectamine was purchased from Invitrogen. RSF1, PTGS2, CFLAR, XIAP, BCL2, BCL2L1, and GAPDH (glyceraldehyde-3-phosphate dehydrogenase) oligonucleotide primers were purchased from Bioneer Technology. Paclitaxel was purchased from A.G. Scientific, Inc. The IκB inhibitor Bay 11-7082 and the proteasome inhibitor MG132 were obtained from Calbiochem. PureProteome protein A magnetic beads were purchased from Millipore.
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5

RNA Extraction and Real-Time qRT-PCR Analysis

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Total RNA was isolated from WJ-MSCs using an AccuPrep Universal RNA Extraction kit (Bioneer), according to the manufacturer's protocol. Real-time qRT-PCR was performed with a QuantStudio 6 Flex Real-Time PCR System (Thermo Fisher Scientific Inc., Waltham, MA, USA) and 2x Power SYBR Green Master Mix (Applied Biosystems, Waltham, MA, USA) using the following program: 95°C for 10 min, followed by 40 cycles of 95°C for 15 s, 56°C for 30 s, and 72°C for 30 s. Primers were purchased from Bioneer Corporation, and the primer sequences were as follows: AURKA, forward 5′-GGCCACTGAATAACACCCAAA-3′ and reverse 5′-AGAGGGCGACCAATTTCAAAG-3′; DOCK2, forward 5′-TTTCAACACCGTTCTGGAGG-3′ and reverse 5′-TCAGCGTTCTTAGGATTGGC-3′; and GAPDH, forward 5′-GAAGGTGAAGGTCGGAGT-3′ and reverse 5′-TGGCAACAATATCCACTTTACCA-3′. All PCR reactions were performed in triplicate, and comparative quantification of each target gene was normalized to GAPDH expression using the 2-ΔΔCt method.
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6

Methanol Extraction of P. attenuatum and Anti-inflammatory Effects

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Methanol extraction of P. attenuatum (Pa-ME) was purchased from the Plant Extract Bank in the Plant Diversity Research Center (Daejeon, Republic of Korea; http://extract.kribb.re.kr, e-mail: mplantext@kribb.re.kr). RAW264.7 cells, a transformed macrophage cell line derived from the BALB/c mouse (ATCC number TIB-71), were purchased from ATCC (Rockville, MD, USA). Dimethyl sulfoxide (DMSO), L-NG-nitroarginine methyl ester (L-NAME), indomethacin, lipopolysaccharide (LPS, Escherichia coli 0111:B4), pam3CSK, and (3-4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) were purchased from Sigma Chemical Co. (St Louis, MO, USA). Poly I:C was obtained from Calbiochem (La Jolla, CA). The enzyme immune assay (EIA) kits used to quantitate the levels of PGE2 were purchased from Amersham (Little Chalfont, Buckinghamshire, UK). Specific PCR primers for iNOS, TNF-α, COX-2, and GAPDH were synthesized from Bioneer Inc. (Daejeon, Republic of Korea). Antibodies that specify phosphorylated and total forms of p65, p50, c-Jun, c-Fos, Lamin A/C, IκBα, IKKα/β, AKT, Src, Syk, ERK, p38, JNK, IRAK1, IRAK4, TAK1, MKK3/6, and β-actin were obtained from Cell Signaling (Beverly, MA, USA).
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7

Adipogenic Differentiation Assay Protocol

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Isobutyl methyl xanthine (IBMX), dexamethasone (DEX), insulin, Oil red O, and all other chemicals were purchased from Sigma-Aldrich (St. Louis, MO, USA). Dulbecco’s modified eagle’s medium (DMEM), bovine serum (BS), heat-inactivated fetal bovine serum (FBS), and penicillin–streptomycin (PS) were purchased from Life Technologies, Inc. (Grand Island, NY, USA). Antibodies for phospho-adenosine monophosphate-activated protein kinase α (p-AMPKα), AMPK, phospho-acetyl-CoA carboxylase (p-ACC), ACC, extracellular signal-regulated kinases (ERK), c-Jun N-terminal kinases (JNK), PPARγ, C/EBPα, and β-actin were purchased from Santa Cruz Biotechnology, Inc. (Santa Cruz, CA, USA). Horseradish peroxidase-conjugated secondary antibodies were obtained from Jackson Immuno Research laboratories, Inc. (West Grove, PA, USA). SYBRTM Green PCR Master Mix was purchased from Applied BiosystemsTM (Foster City, CA, USA). Oligonucleotide primers of PPAR-γ, SREBP1, C/EBPα, and GAPDH were purchased from Bioneer (Daejeon, Chungbuk, Republic of Korea).
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8

RAW264.7 Cell Inflammatory Response Assay

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RAW264.7 cells from mice (BLAB/c, ATCC number TIB-71) were purchased from ATCC (Rockville, MD, USA). Dimethyl Sulfoxide (DMSO), L-NG–nitroarginine methyl ester (L-NAME), lipopolysaccharide (LPS, Escherichia coli 0111:B4), and (3-4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) were purchased from Sigma Chemical Co. (St Louis, MO, USA). Gene specific PCR primers for iNOS, TNF-α, COX-2, and GAPDH were synthesized from Bioneer Inc. (Daejeon, Republic of Korea). Antibodies to phosphorylated and total protein (p65, p50, IκBα, IKKα/β, Syc, Syk, STAT3, JAK, and β-actin) were obtained from Cell Signaling (Beverly, MA, USA).
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9

Total RNA Extraction and qRT-PCR Analysis

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Total RNAs from cells were extracted using the RiboEx Total RNA solution (GeneAll Biotechnology, Seoul, Korea). Cells in 6-well plates (0.5 mL, 1 × 105 cells per well) were transferred to tubes, to which chloroform (0.1 mL) was added, and shaken vigorously for 30 s. Aqueous phases were transferred to fresh tubes, and an equal volume of isopropanol was added. Samples were then incubated for 15 min at 4 °C and centrifuged at 12,000× g for 15 min at 4 °C. After discarding the supernatants, RNA pellets were washed once with 0.5 mL of 75% ethanol, vortexed briefly, and centrifuged at 7500× g for 5 min at 4 °C. Pellets were dried for 10–15 min and dissolved in diethyl pyrocarbonate (DEPC)-treated water. Complementary DNA (cDNA) was synthesized from the total RNA (2 µg) using SuPrime Script RT Premix with random hexamer cDNA Synthesis Kit (GeNet Bio, Daejeon, Korea), in accordance with the manufacturers’ instructions. Quantitative qRT-PCR amplification was performed using SensiFASTTM SYBR® No-ROX dye (Bioline, London, UK) on the CFX Connect System (Bio-Rad Laboratories, Hercules, CA, USA). The primers specific to TRP-1, TRP-2, tyrosinase, or GAPDH were purchased from Bioneer Inc. (Daejeon, Korea). Relative gene expressions were assessed using GAPDH as the internal control. The primer sequences used in this study are shown in Table 1.
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10

Relative gene expression analysis

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Oligonucleotide primers specific for glyceraldehyde 3-phosphate dehydrogenase (GAPDH), SREBP-1c, C/EBPα, PPARγ, UCP-1, αSMA, and Col1α1 were purchased from Bioneer (Daejeon, Korea). M-MLV reverse transcriptase and random Oligonucleotide primers were from Promega (Fitchburg, WI, USA). TOP script RT Dry MIX was from Enzynomics Co., Ltd. (Daejeon, Korea). Thunderbird SYBR quantitative polymerase chain reaction (qPCR) Mix was from TOYOBO Co., Ltd. (Osaka, Japan). All other chemicals were from Sigma-Aldrich Chemical Co. (St. Louis, MO, USA).
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