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Trizol reagent

Manufactured by Corning
Sourced in China, United States

TRIzol reagent is a ready-to-use reagent for the isolation of total RNA, DNA, and proteins from a variety of biological samples. It is based on a monophasic solution of phenol, guanidine isothiocyanate, and other proprietary components that facilitate the separation of the sample into an aqueous phase containing RNA, an interphase containing DNA, and an organic phase containing proteins.

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10 protocols using trizol reagent

1

RNA Extraction and cDNA Cloning Protocol

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Viral RNA samples were extracted using Trizol reagent (Axygen, China), according to the manufacturer’s instructions. RNA was eluted into RNAse-free ddH2O and stored at − 80 °C until use. In this study, reverse transcription reactions of extracted RNA were performed with a PrimeScript™ 1st Strand cDNA Synthesis Kit (TaKaRa, Dalian, China).
The target fragment was obtained by amplification of cDNA with conventional primer and cloned into a pMD19-T vector (Takara, Dalian, China). The recombinant vector was transformed into DH5α Escherichia coli cells and shaken overnight at 37 °C; the cells were then purified with plasmid Mini Kit2 (Omega BioTek, USA), according to the manufacturer’s recommendations (Takara, Dalian, China). The positive recombinant plasmids were confirmed through sequencing analysis (Takara, Dalian, China). The recombinant plasmid concentrations were measured with UV spectrophotometry (NanoDrop one) and converted into copy numbers. The plasmid DNA was stored at − 80 °C until further use.
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2

RNA Extraction and Gene Expression Profiling

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RNA was extracted by using the TRIzol™ Reagent (Thermo Fisher, Waltham, MA, USA) according to the manufacturer’s protocol. In short, up to 100 mg of brain tissue was homogenized by applying tissue grinders (Axygen™, Union City, CA, USA) and 1 mL of TRIzol™ Reagent, followed by a phase separation step where chloroform was used. RNA was precipitated with isopropyl alcohol. The quantity and quality of the RNA-extracts were monitored applying a NanoDrop 2000 Spectrophotometer (Thermo Scientific™, Waltham, MA, USA) and 2100 Bioanalyzer (Agilent Technologies) together with RNA 6000 Nano kit. The amount of RNA received from samples was between 21–71 μg, the A260/280 ratio was between 1.87–2.01, the A260/230 ratio was between 1.98–2.21, the average RIN value of RNA samples was 4.389 ± 0.456 (mean ± SD). Throughout the RNA extraction Eppendorf DNA/RNA LoBind tubes were applied (Sigma-Aldrich, St. Louis, MO, USA).
For each sample, 100 ng RNA input was taken for gene expression analysis. Gene expression profiling was conducted with Affymetrix GeneTitan Multi-Channel platform with Clariom S human microarray and GeneChip WT (whole transcriptome) Plus kit (Affymetrix Inc, Santa Clara, VA, USA) according to the manufacturer’s protocol. Clariom S microarray provides data for more than 20,000 well-annotated genes.
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3

Quantitative RT-PCR Analysis of Aquaporin and Cytokine Expression in HK-2 Cells

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Total RNA was extracted from HK-2 cells using TRIzol reagent (Axygen; Corning Incorporated, Corning, NY, USA) according to the manufacturer's protocols. Purifed RNA (0.5 µg/µl) was mixed with nuclease-free water for the cDNA synthesis using a Script cDNA Synthesis kit (Bio-Rad Laboratories, Inc., Hercules, CA, USA) at 37°C for 15 min and 85°C for 5 sec. RT-qPCR was performed using a Bio-Rad CFX96 real-time PCR System (Bio-Rad Laboratories, Inc.). The qPCR reaction volume was 50 µl and included 1 µl dNTPs (10 mM), 5 µl cDNA solution, 1 µl of each primer (50 pM), 1 µl Taq DNA polymerase (Invitrogen; Thermo Fisher Scientific, Inc.), 33 µl water, 3 µl of MgCl2 (15 mM), and 5 µl of PCR buffer (10X). The amplification was performed according to the following condition: Denaturation was performed at 94°C for 1 min, annealing at 59°C for 1 min and elongation at 72°C for 1 min for 32 cycles, followed by 72°C for 10 min. The expression of AQP-1, AQP-2, AQP-3, AQP-4, AQP-6, AQP-7, AQP-8, AQP-11, TNF-α, IL-8, IL-1β and MCP-1 was detected by using the SYBR-Green PCR kit (Takara Bio, Inc., Otsu, Japan). Primers are listed in Table I and GAPDH was used as an internal reference. Results were normalized using the 2−ΔΔCq method (16 (link)) and each experiment was performed in triplicate.
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4

Quantifying AQP1 Expression in Mouse Tissues

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Total RNA was extracted from mouse kidney tissues and RAW264.7 cells using TRIzol reagent (Axygen; Corning Incorporated, NY, USA) according to the manufacturer’s protocol. Purified RNA (1 µg/µl) was reverse-transcribed into cDNA using a Script cDNA Synthesis Kit (Bio-Rad Laboratories, Inc., CA, USA) at 37 °C for 15 min and at 98 °C for 5 min. RT-qPCR was carried out using a Bio-Rad CFX96 Optics Real-Time PCR System (Bio-Rad Laboratories, Inc., CA, USA). cDNA was amplified by polymerase chain reaction using specific primers (Table 1). The following PCR conditions were used for AQP1 and β-actin: 40 cycles of denaturation at 95 °C for 5 s, annealing at 60 °C for 10 s, and extension at 72 °C for 15 s. The AQP1 and β-actin primers produced amplified products of 129 and 70 bp, respectively.

Primers used in the qPCR analysis

PrimerSequence
AQP1Forward primer 5′-CCTGCTGGCCATTGACTACA-3′
AQP1Reverse primer 5′-TGGTTTGAGAAGTTGCGGGT-3′
β-ActinForward primer 5′-CGCGAGTACAACCTTCTTGC-3′
β-ActinReverse primer 5′-CGTCATCCATGGCGAACTGG -3′
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5

RNA Extraction and Gene Expression Analysis

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Total tissue RNA was separated by TRIzol reagent (Corning, USA), cDNA was retrieved and mRNA expression was measured using the SYBR Premix EX Taq II kit (Takara, Japan), and the 2−△△Ct method was adopted to analyse relative gene expression.
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6

Quantitative Real-Time PCR Analysis of ER Stress Markers

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Total RNA was extracted from liver tissues using TRIzol™ reagent (Corning Life Sciences Co., Ltd., Jiangsu, China) and reversely transcribed to cDNA using the Primescript™ RT Master Mix Kit (Takara; RR036A). Transcript levels were measured in duplicate by qRT-PCR (Bio-Rad) using SYBR Green I (Takara Biotechnology, Dalian, China). Expression levels were normalized to β-actin. Primer sequences are listed in Table 1.

The Sequences of Primers Used for Real-Time Quantitative PCR

GenesForward Primer (5’-3’)Reverse Primer (5’-3’)
GRP78TGTGTGTGAGACCAGAACCGAACACACCGACGCAGGAATA
ChopCCTGAGGAGAGAGTGTTCCAGGACACCGTCTCCAAGGTGAA
β-actinGTGCTATGTTGCTCTAGACTTCGATGCCACAGGATTCCATACC
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7

TMEM92 Protein and mRNA Analysis

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Proteins were extracted from cells using RIPA lysis buffer with proteinase inhibitor. Then, proteins were separated by SDS-PAGE and transferred to polyvinylidene fluoride (PVDF) membranes. The membranes were blocked with 5% milk and 0.01% Tween-20 in tris-buffered saline (TBS; pH 7.6) and incubated with TMEM92 antibody diluted at 1:500 in TBS overnight at 4°C. GAPDH was used as an internal control. Protein quantification was performed in ImageJ.
RNA extraction and cDNA synthesis were performed using the TRIzol reagent (Corning co, USA) and PrimeScript RT Reagent Kit (Promega, Beijing, China), respectively. mRNA expression levels of TMEM92 were quantified using the SYBR Premix Ex Taq system (Promega, Beijing, China), with glyceraldehyde-3-phosphate dehydrogenase (GAPDH) expression levels serving as a normalization control. The relative levels of TMEM92 were determined using the comparative quantification cycle (Cq) method (2−ΔΔCq) based on three repeated measurements. The primers used in this study are listed below:
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8

Investigating Anti-inflammatory Effects of DHL

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RAW264.7 cells (5 × 105) were challenged with LPS for 24 h followed incubation with DHL (0, 3, 5, 15 and 30 μmol/L) for 30 mins. The lung macrophages were challenged with LPS for 8 h and 16 h followed incubation with DHL (0, 3, 5, 15 and 30 μmol/L) for 30 mins. Lung tissues from LPS induced mice model with or without DHL treatment were collected and homogenized. Total RNA were extracted using TRIzol reagent (Corning, Shanghai, China). cDNA was was synthesized by ReverTra Ace qPCR RT Kit (Toyobo, Osaka, Japan) and amplified by realtime PCR on a StepOne Plus system (Thermo Fisher Scientifc, Waltham, MA, USA) with primer sets for iNOS (forward, 5′-CCCTTCAATGGTTGGTACATGG-3′; reverse, 5′-ACATTGATCTCCGTGACAGCC-3′), TNF-α (forward, 5′-TTCTCATTCCTGCTTGTGG-3′; reverse, 5′-ACTTGGTGGTTTGCTACG-3′), IL-6 (forward, 5′-CCACCAAGAACGATAGTCAA-3′; reverse, 5′-TTTCCACGATTTCCCAGA-3′), IL-12p35 (forward, 5′- GGACCAAACCAGCACAT-3′; reverse, 5′- CGCAGAGTCTCGCCATTA-3′), IL-12p40 (forward, 5′- TGAACTGGCGTTGGAAG-3′; reverse, 5′- GAAGTAGGAATGGGGAGTG-3′), IL-1β (forward, 5′-CCAGCTTCAAATCTCACAGCAG-3′; reverse, 5′-CTTCTTTGGGTATTGCTTGG GATC-3′), and GAPDH (forward, 5′-TGCGACTTCAACAGCAACTC-3′; reverse, 5′-CTTGCTCAG TGTCCTTGCTG-3′). The relative expression (defined as fold change) of target gene was given by 2-△△Ct and normalized to the GAPDH.
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9

Quantifying Orexin A Expression in Mice

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After polygraphic recordings and sleep–wake states analysis were done, hypothalamus tissues of mice (10 were chosen from each group randomly) were collected and homogenized. Total RNA was extracted using TRIzol reagent (Corning, Shanghai, China). cDNA was synthesized using ReverTra Ace qPCR RT Kit (Toyobo, Osaka, Japan) and amplified by real-time PCR on a StepOne Plus system (Thermo Fisher Scientific, Waltham, MA, USA) with primer sets for Orexin A (forward, 5′- GCCTCAGACTTCTTGGGTATTT-3′; reverse, 5′- AGGGAACCTTTGTAGAAGGAAA -3′) and GAPDH (forward, 5′-TGCGACTTCAACAGCAACTC-3′; reverse, 5′-CTTGCTCAGTGTCCTTGCTG-3′). The relative expression (defined as fold change) of the target gene was given by 2−△△Ct and normalized to GAPDH. At least triplicate independent experiments were performed.
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10

Quantifying Hypothalamic Gene Expression

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After polygraphic recordings and sleep-wake states analysis were done, hypothalamus tissues of mice (10 were chosen from each group randomly) were collected and homogenized. Total RNA was extracted using TRIzol reagent (Corning, Shanghai, China). cDNA was synthesized using ReverTra Ace qPCR RT Kit (Toyobo, Osaka, Japan) and ampli ed by real-time PCR on a StepOne Plus system (Thermo Fisher Scienti c, Waltham, MA, USA) with primer sets for Orexin A (forward, 5'-GCCTCAGACTTCTTGGGTATTT-3'; reverse, 5'-AGGGAACCTTTGTAGAAGGAAA -3') andGAPDH (forward, 5'-TGCGACTTCAACAGCAACTC-3'; reverse, 5'-CTTGCTCAGTGTCCTTGCTG-3'). The relative expression (de ned as fold change) of the target gene was given by 2 -△△Ct and normalized to GAPDH. At least triplicate independent experiments were performed.
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