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30 protocols using ultrasybr mixture

1

Quantification of METTL3 mRNA in Ovarian Cancer

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Total RNA of human ovarian cancer cells was prepared using an Ultrapure RNA Extraction kit (CWBio) according to the manufacturers protocol. A total of 1 µg RNA was reverse-transcribed into cDNA with random primers using a HiFiScript cDNA Synthesis kit (CWBio) according to the manufacturers protocol. The reverse transcription reaction conditions were as follows: incubation at 42°C for 50 min, followed by incubation at 85°C for 5 min to terminate the reaction. METTL3 mRNA expression levels were determined by fluorescence qPCR using UltraSYBR mixture (CoWin Biosciences) according to the manufacturers protocol and an Applied Biosystems 7500 FAST Real-time PCR system (Applied Biosystems; Thermo Fisher Scientific, Inc.). The following thermocycling conditions were used for qPCR: Initial denaturation at 95°C for 30 sec; 40 cycles of 95°C for 5 sec, 60°C for 30 sec and one cycle of melting curve at 95°C for 15 sec, 60°C for 1 min, 95°C for 15 sec and 50°C for 30 sec. Quantification of METTL3 mRNA expression levels was performed using the 2−ΔΔCt method (10 (link)) with β-actin as an internal control. The sequences of primers were as follows: METTL3 forward, 5′-ACCCTGACAGATGATGAGATGC-3′ and reverse, 5′-CGTTCATACCCCCAGAGGTTTAG-3′; β-actin forward, 5′-TCCTCCCTGGAGAAGAGCTAC-3′ and reverse, 5′-TCCTGCTTGCTGATCCACAT-3′.
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2

miRNA-218-5p Expression Analysis

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After the transfection for 24 hours, total RNA was extracted using TRIzol reagent (Invitrogen, USA) and reverse transcribed to cDNA using a HiFiScript cDNA Synthesis Kit (CoWin Biotech Co. Ltd., China). MiRNA was extracted using an miRNA Purification Kit (CoWin Biotech Co. Ltd., China) and reverse transcribed to cDNA using an miRNA cDNA Synthesis Kit (CoWin Biotech Co. Ltd., China). UltraSYBR Mixture and miRNA qPCR Assay Kit (CoWin Biotech Co. Ltd., China) were used for qPCR according to the manufacturer’s protocol. The following primers were used in this study, miR-218-5p (5ʹ-TTGTGCTTGATCTAACCATGT-3ʹ), NACC1-Forward (5ʹ-GCCTGTACTGTGACGTGTCA-3ʹ) and NACC1-Reverse (5ʹ-CGTGGAGAACTTGGCCATCT-3ʹ). The relative expressions of genes were calculated using the 2−ΔΔCt method.
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3

Evaluation of UA232 in ER Stress-Induced Apoptosis

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UA232 was synthesized in our laboratory with a purity of > 98%. UA, 3-methyladenine (3-MA), and CA-074 methyl ester (CA-074-me) were purchased from MedChemExpress (Monmouth Junction, NJ, USA), and 4-phenylbutyric acid (4-PBA) was purchased from Energy Chemical (Shanghai, China). Crystal violet, 4',6-diamidino-2-phenylindole dihydrochloride (DAPI), 4% paraformaldehyde fix solution, Lyso-Tracker Red dye, and Cell Counting Kit-8 (CCK-8) were purchased from Beyotime Biotechnology (Shanghai, China). The cell cycle detection kit and Annexin V-FITC/PI kit were purchased from KeyGen Biotech (Nanjing, China). Primary antibodies against cyclin D1, CDK4, Bax, Bcl-2, caspase-8, caspase-3, PARP1, CHOP, GRP78, ATF4, LC3, P62, and LAMP2 were purchased from Proteintech Group (Rosemont, IL, USA). Antibodies against PERK, p-PERK, eIF2a, and p-eIF2a were purchased from Bioss (Beijing, China). Antibodies against cathepsin B were purchased from Abcam (Cambridge, MA, USA). β-actin, horseradish peroxidase conjugated secondary antibodies (goat anti-mouse or goat anti-rabbit), and fluorescently labeled secondary antibodies (IgG Alexa Fluor® 488 or 594 goat-anti-rabbit) were obtained from ZSGB BIO (Beijing, China). Trizol reagent, cDNA synthesis kit, and UltraSYBR mixture were purchased from CoWin Biotech (Beijing, China).
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4

Comprehensive RNA Extraction and qRT-PCR

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Total RNA was isolated using Trizol reagent (Sigma Aldrich), RNA concentration was measured by a NanoDrop spectrophotometer (Thermo Fisher Scientific), and then cDNA was synthesized using HiFi Script cDNA Synthesis Kit (Cowin Biotech, Beijing, China) or miRcute Plus miRNA First-Strand cDNA Kit (Tiangen Biotech, Beijing, China).
The qRT-PCR was conducted by Ultra SYBR Mixture (Cowin Biotech). β-Actin (for circRNA) and U6 (for miRNA) were internal controls. Relevant primers involved in the current experiments were designed from Tsingke Biotechnology (Beijing, China), and the sequences of primers are shown in Table 2.
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5

Quantification of miRNA and mRNA Levels

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Total RNA was extracted from isolated PBMCs and DAKIKI cells with TRIzol Reagent (Invitrogen, CA, United States). Reverse Transcription Systems (for miRNA: CW2141, for mRNA: CW2569, CoWin Biosciences, Beijing, China) were used to reverse transcribe 1 μg of total RNA into cDNA. Levels of miR-98-5p, miR-152-3p, and C1GALT1, were then determined by qRT-PCR using the UltraSYBR Mixture (CW2601, CoWin Biosciences, Beijing, China) on a qRT-PCR detection system (Thermo Fisher, Pikoreal96, United States). Primers are shown in Supplementary Table S1. U6 snRNA and β-actin were used for normalization. Gene expression levels were calculated by the 2−ΔΔCT method. All experiments were replicated three times.
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6

Gene Expression Analysis of Peripheral Blood Cells

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RNA of peripheral blood mononuclear cells was extracted by EZ-10 Total RNA Mini-Preps Kit (Sangon Biotech, Shanghai, China) and subjected to reverse transcription using HiFiScript cDNA Synthesis Kit (CoWin Biosciences, Beijing, China). The messenger RNA levels were assessed by quantitative real‐time PCR using UltraSYBR Mixture (CoWin Biosciences, Beijing, China). β-actin was used as the internal control. The primers used in the study were as follows: β-actin, 5′‐AGA GGG AAA TCG TGC GTG AC‐3′ (sense) and 5′‐CAA TAG TGA TGA CCT GGC CGT‐3′ (antisense); CCR7, 5′‐TGT ACG AGT CGG TGT GCT TC ‐3′ (sense) and 5′‐GGT AGG TAT CCG TCA TGG TCT TG‐3′ (antisense); KLRK1, 5′‐ACT CAG AGA TGA GCA AAT GCC‐3′ (sense) and 5′‐CAG GTT GAC TGG TAG TTA GTG C‐3′ (antisense); TIGIT, 5′‐ CCA CAG CAG GCA CGA TAG ATA ‐3′ (sense) and 5′‐CCA CCA CGA TGA CTG CTG T‐3′ (antisense); Slamf1, 5′‐CAG AAA TCA GGG CCT CAA GAG‐3′ (sense) and 5′‐ CAT GCC ACC CCA GGT CAA C ‐3′(antisense).
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7

RNA Extraction and qPCR Analysis

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TRIzol® reagent (Invitrogen; Thermo Fisher Scientific, Inc.) was used to extract total RNA from the cultured HPC, HPC-NC or HPC-C3a cells. cDNA was generated using a PrimeScriptTM RT Master Mix kit (Takara Biotechnology Co., Ltd.), according to the manufacturer's protocol, and analyzed by RT-qPCR using 1 µl of cDNA, 250 nM primers and UltraSYBR mixture (CoWin Biosciences). 18S RNA was used as the endogenous control. The sequences of the primers are presented in Table I. The following thermocycling conditions were used to detect the expression levels of nephrin: Initial denaturation at 95°C for 5 min; followed by 40 cycles of 95°C for 20 sec, 58°C for 10 sec and 72°C for 45 sec; and a final extension at 72°C for 5 min. The following thermocycling conditions were used for the rest of the genes: Initial denaturation at 95°C for 5 min; followed by 40 cycles of 95°C for 20 sec, 60°C for 20 sec and 72°C for 30 sec; and a final extension at 72°C for 5 min. The expression levels were quantified using the 2−∆∆Cq method (23 (link)) and finally normalized to the expression levels of in the HPC control cells (which was set to 1.0).
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8

Quantification of TRAP1 Expression

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Total RNA was isolated by using TRIZOL reagent (Invitrogen) and the phenol-chloroform extraction method according to manufacturer protocols. The cDNA was synthesized using a First-Strand cDNA Synthesis Kit (Invitrogen). Quantitative real-time PCR was performed on an ABI 7300 instrument with UltraSYBR Mixture (CoWin Biosciences) according to manufacturer instructions with the following primers: GAPDH, forward: 5′-AGGCTGAGAACGGGAAGC-3′, reverse: 5′-CCATGGTGGTGAAGACGC-3′; TRAP1, forward: 5′-CGCAGCATCTTCTACGTGC-3′; reverse: 5′-CTGATGAGTGCGCTCTCC-3′.
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9

RNA Extraction and Expression Analysis of MEG3 and miR-9-5p

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Total RNA was extracted from MHCC-97L cells using the Ultrapure RNA kit (CoWin Biosciences), and then reverse-transcribed into cDNA using a HiFiScriptcDNA synthesis kit (CoWin Biosciences). Reverse transcription was performed at 50°C for 15 min, and then at 85°C for 5 min. Primers used for amplification were: MEG3 forward, 5′-CATACAAAGCAGCCACTCAC-3 and reverse, 5′-GGGATCCTTCCATTCAGGAC-3′; GAPDH forward, 5′-CAATGACCCCTTCATTGACC-3 and reverse, 5′-GAGAAGCTTCCCGTTCTCAG-3′; miR-9-5p forward, 5′-TCTTTGGTTATCTAGCTGTATGA and reverse, 5′-CCAGCTATGCGCCATTAGCAA-3′; U6 forward, 5′-GCTTCGGCAGCACATATACTAAAAT-3 and reverse, CGCTTCACGAATTTGCGTGTCAT-3′ (CoWin Biosciences). RT-qPCR assays were performed using the UltraSYBR Mixture (CoWin Biosciences). Data were analyzed using the 2−ΔΔCq method (23 (link)). Expression of MEG3 was normalized to GAPDH, and expression of miR-9-5p was normalzed to U6.
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10

Gene Expression Analysis in Adipogenic Cells

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Total RNA was extracted from cells using Trizol reagent (Invitrogen™, Thermo Fisher Scientific) according to the manufacturer’s instructions. After quantification, cDNA was obtained using the Reverse Transcription System (Promega, Corporation, Fitchburg, MA, USA), with oligo (dT) primer for mRNA and stem-loop reverse transcription primer for miRNA. The mRNA expression level of genes was examined by RT-qPCR using UltraSYBR Mixture (CoWin Biosciences, Beijing, China) with the following pairs of primers: PPARγ forward, 5′-TGTGGGGATAAAGCATCAGGC-3′, and reverse 5′-CCGGCAGTTAAGATCACACCTAT-3′; C/EBPα forward, 5′-GCTGGAGTTGACCAGTGACA-3′, and reverse 5′-AAACCATCCTCTGGGTCTCC-3′; C/EBPβ forward, 5′-GCAAGAGCCGCGACAAG-3′, and reverse 5′-GGCTCGGGCAGCTGCTT-3′; FABP4 forward, 5′-ACACCGAGATTTCCTTCAAACTG-3′, and reverse 5′-CCATCTAGGGTTATGATGCTCTTCA-3′; c-Met forward, 5′-ACCAAGTGCTCCTGACATCC-3′, and reverse 5′-GTGAGGTGTGCTGTTCGAGA-3′;GAPDH forward, 5′-AAGAAGGTGGTGAAGCAG-3′, and reverse 5′-GAAGGTGGAAGAGTGGGAGT-3′; U6 snRNA forward, 5′-CTCGCTTCGGCAGCACA-3′, and reverse 5′-AACGCTTCACGAATTTGCGT-3′; mmu-miR-206-3p forward, 5′-ACACTCCAGCTGGGTGGAATGTAAGGAAGTGT-3′, and reverse 5′-TGGTGTCGTGGAGTCG-3′. Relative quantification (2−ΔΔCt) method was used to analyze the data, GAPDH mRNA was used as reference for mRNA quantification, and U6 snRNA was used for miRNA.
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