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14 protocols using qrt supermix

1

Quantitative Analysis of TNMD and LINC00656 Expression

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Total RNA was extracted using the RNA Isolation Kit (Vazyme, China) and reversely transcribed to cDNA using the qRT SuperMix (Vazyme, China). The SYBR qPCR Master Mix (Vazyme, China) was used to perform quantitative real-time polymerase chain reaction (qRT-PCR) to assess the transcript levels of TNMD and LINC00656. All study protocols were conducted following the manufacturer’s instructions. Glucuronidase beta (GUSB) was used as internal reference. The sequences of primers included in this study were listed as follows: GUSB: forward primer: 5’- GTCTGCGGCATTTTGTCGG-3’; reverse primer: 5’- CACACGATGGCATAGGAATGG-3’, LINC00656: forward primer: 5’- TGCTCTTTGGACTGAGCTGG-3’; reverse primer: 5’- GTAACGGTGACTGAGACGCA-3’, TNMD: forward primer: 5’- TGTGGACTGGTGTTTGGTATCC-3’; reverse primer: 5’- AGTGCCATTTCCGCTTCTGAA-3’.
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2

Quantitative gene expression analysis

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Total RNA was extracted using a TaKaRa minibest universal RNA extraction kit, and cDNAs were synthesized using HiScript Q RT supermix for quantitative qPCR (+ gDNA wiper; R123-01; Vazyme). qPCR was performed using Accupower Super qPCR kit (APS01; SibEnzyme) on an ABIPRISM7700 system (Applied Biosystems, USA). ACTIN2 was used as an internal control in the analysis of the qRT-PCR data from whole leaves. The qPCR primers included S3H-qPCR-F (5′-TTCATCGTCAATATCGGCGAC-3′) and S3H-qPCR-R (5′-ATCGATAACCGCTCGTTCTCG-3′) for S3H, PR1-qPCR-F (5′-CGAAAGCTCAAGATAGCCCACA-3′) and PR1-qPCR-R (5′-TTCTGCGTAGCTCCGAGCATAG-3′) for PR1, PR2-qPCR-F (5′-GCTTCCTTCTTCAACCACACAGC-3′) and PR2-qPCR-R (5′-CGTTGATGTACCGGAATCTGAC-3′) for PR2, ACTIN2-qPCR-F (5′-GGTAACATTGTGCTCAGTGGTGG-3′) and ACTIN2-qPCR-R (5′-CTCGGCCTTGGAGATCCACATC-3′) for ACTIN2.
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3

Quantitative RNA Expression Analysis

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Total RNA was isolated using TRIzol (Sigma-Aldrich, T9424-100 m), and cDNA was obtained with HiScript Q RT SuperMix for quantitative real-time polymerase chain reaction qRT-PCR (+gDNA wiper) (Vazyme, R123-01). PCRs were performed on an ABI 7500 qRT-PCR machine. GAPDH was used as an endogenous control. We assessed the qualified expression by employing the 2-ΔΔCt formula, while statistical analysis was conducted by using the fold change. All primer sequences used in this research are available in Table 2.
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4

Quantifying Gene Expression in Kidney Cells

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Total RNA was extracted from HK-2 cells or mice kidney tissue using TRIzol® Reagent. Complementary-DNA was synthesized by Hiscript Q RT SuperMix and used for a qPCR (+ gDNA wiper) reverse transcriptase kit (Vazyme). Real-time PCR was undertaken on primers, the sequences of which are shown in Table 1. Messenger (m)RNA expression of the corresponding samples was normalized with GAPDH mRNA.

Primer sequences used for RT-qPCR

GeneForward (5’ to 3’)Reverse (5’ to 3’)
Mus Collagen IGACGCCATCAAGGTCTACTGACGGGAATCCATCGGTCA
Mus α-SMAACTGGGACGACATGGAAAAGGTTCAGTGGTGCCTCTGTCA
Mus SIRT3CACGTTTACAAACATGAACCCATGCTAGATTGCCCTAGT
Mus IL-6GAGGATACCACTCCCAACAGACCAAGTGCATCATCGTTGTTCATACA
Mus IL-1βGACCTTCCAGGATGAGGACAAGCTCATATGGGTCCGACAG
Mus TNF-αCGTCGTAGCAAACCACCAAGTTGAAGAGAACCTGGGAGTAGACA
Mus GAPDHACCCAGAAGACTGTGGATGGACACATTGGGGGTAGGAACA
Hum Collagen ITGACCTCAAGATGTGCCACTACCAGACATGCCTCTTGTCC
Hum α-SMACCCGGGACTAAGACGGGAATCCATCACCCCCTGATGTCTG
Hum SIRT3GAGGTTCTTGCTGCATGTGGTTGAGTTTCCCGCTGCACAAGGTC
Hum IL-6CTGCAGCCACTGGTTCTGTCCAGAGCTGTGCAGATGAGT
Hum IL-1βCGATGCACCTGTACGATCACTCTTTCAACACGCAGGACAG
Hum TNF-αTGCACTTTGGAGTGATCGGCACTCGGGGTTCGAGAAGATG
Hum GAPDHTGATGACATCAAGAAGGTGGTGAAGTCCTTGGAGGCCATGTGGGCCAT

Mus mouse, Hum human, SIRT3 sirtuin 3

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5

Quantification of Gene Expression via RT-PCR

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Total RNA was extracted from cells using TRIzol reagent (Invitrogen, Carlsbad, USA) according to the manufacturer’s instructions. The reverse transcription of 1 μg RNA was carried out using qRT SuperMix (Vazyme, Nanjing, China). A real-time-polymerase chain reaction (RT-PCR) analysis was carried out using the ABI Stepone Plus system with the AceQ SYBR Green Master Mix (Vazyme, Nanjing, China). The primers were synthesized by Bioneer, and the primer sequences for the human genes were: VE-cadherin, 5′-CCAGAATTTGCCCAGCCTA-3′ and 5′-TTACTGGCACCACGTCCTTGTC-3′; Vimentin, 5′-TGCCGTTGAAGCTGCTAACTA-3′ and 5′-CCAG-AGGGAGTGAATCCAGATTA-3′; Nrf2, 5′-TTCCCGGTCACAT-CGAGAG-3′ and 5′-TCCTGTTGCATACCGTCTAAATC-3′; Smad7, 5′-GGACAGCTCAATTCGGACAAC-3′ and 5′-GTACACCCACACACCATCCAC-3′; β-actin, 5′-AAGACCTGTACGCCAACACAGT-3′ and 5′-AGAAGCATTTGCGGTGGACGAT-3′. Amplified expressions of gene transcriptions were normalized to β-actin expression. Cycle threshold (ΔΔCt) values were calculated for each experimental group, which indicated the number of available template cDNA in each reaction. The gene expression levels were compared using values of 2−ΔΔCt.
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6

RNA Extraction and qPCR Analysis Protocol

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Total RNA was extracted using the Trizol method (Sigma-Aldrich). RNA was purified and reverse-transcribed to cDNA with Q RT SuperMix (Vazyme#R223, Nanjing, China). qPCR analysis was performed with a ChamQ Universal SYBR qPCR Master Mix (Vazyme#Q711) according to the manufacturer’s instructions in a Bio-Rad CFX96 Touch q-PCR system. The GAPDH gene was used as an endogenous control. All the primers are shown in Supplementary Table S1.
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7

RT-qPCR Analysis of 15 Selected Genes

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A total of 15 genes were selected for RT-qPCR analysis. First-strand cDNA was synthesized from total RNA using HiScript II Q RT Supermix for qPCR with a gDNA wiper (Vazyme R223-01, Nanjing, China). RT-qPCR was performed using the AceQ qPCR SYBR green master mix (Vazyme Q111-02/03, Nanjing, China). The qPCR reactions were performed in a final volume of 10 μL containing 5 μL of 2 × AceQ qPCR SYBR green master mix, 0.25 μL of 10 μM of each primer, 4.25 μL of ddH20, and 0.25 μL of cDNA. Reactions were carried out at 95°C for 5 min, followed by 40 cycles of 95°C for 10 s, 60°C for 30 s, and melting curve analysis from 60°C to 95°C at 1°C increments (qTOWER3G, Jena German). Primers for qPCR were designed based on our predicted gene sequences by NCBI primer blast, and the parameters were modified to suit the RT-qPCR conditions (Supplementary Table 5). The 18S gene was used as an internal control. Fold changes were determined by the 2–ΔΔCt method. All qPCR reactions were run in triplicate.
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8

Analysis of Inflammatory Markers in Lung Tissue

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The total RNA in the lung tissue was harvested using TRIzol reagent (Invitrogen; Thermo Fisher Scientific, Inc.). cDNA was synthesized using qRT SuperMix (Vazyme, JiangSu, China). RT-qPCR was performed with AceQ SYBR-Green Master Mix (Vazyme). The following primers were used for PCR analysis: ICAM-1 forward, 5′-GTGATGCTCAGGTATCCATCCA-3′ and reverse, 5′-CACAGTTCTCAAAGCACAGCG-3′; VCAM-1 forward, 5′-TTGGGAGCCTCAACGGTACT-3′ and reverse, 5′-GCAATCGTTTTGTATTCAGGGGA-3′; TNF-α forward, 5′-GGAACACGTCGTGGGATAATG-3′ and reverse, 5′-GGCAGACTTTGGATGCTTCTT-3′; IL-8 forward, 5′-AGCAGTCCCAACTAAGCAGTA-3′ and reverse, 5′-CAGCCAGTAGAGGATGCTGA-3′; and β-actin forward, 5′-GAGTCCTACGACATCATCGCT-3′ and reverse, 5′-CGTCCGACATAGTTTGGGAAA-3′. The cycle threshold (CT) method was used to analyze the data in each experimental group (19 (link)).
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9

Quantitative RT-PCR Analysis of Lipid Metabolism Genes

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Total RNA was extracted using TRIzol RNA isolation kits (Life Technologies, Grand Island, NY) according to manufacturer’s instructions. cDNA was synthesized using 1 μg of RNA in 20 μL of reaction buffer containing qRT SuperMix (R323-01; Vazyme) and random primers. Real-time PCR was carried out with a qPCR SuperMix kit (Q341-02; Vazyme) according to manufacturer’s instructions. The sequences of the primers were as following: mouse PPARα, 5′-GGA​ACC​CAA​GTT​TGA​CTT​CGC-3′ and 5′-CCC​CTC​CTG​CAA​CTT​CTC​AAT-3’; mouse CPT1A, 5′-CAA​GGT​CTT​CTC​GGG​TCG​AAA-3′ and 5′-CAC​TGC​AAT​TTG​GGT​CCA​AGG-3’; mouse CPT2, 5′-TCC​GCT​TTG​TTC​CTT​CCT​CTC-3′ and 5′-CAT​CAC​GAC​TGG​GTT​TGG​GTA-3’; mouse ACOX1, 5′-AAC​TTC​CTC​ACT​CGA​AGC​CAG-3′ and 5′-AAG​GTC​CAA​AGG​CTC​AGG​ATG-3’; human PPARα, 5′-AAC​GAT​TCG​ACT​CAA​GCT​GGT-3′ and 5′-TGT​GAC​ATC​CCG​ACA​GAA​AGG-3’; human ACOX1, 5′-AAC​CCG​GAG​CTG​CTT​ACA​C-3′ and 5′-GGC​TGC​GAG​TGA​GGA​AGT​T-3’.
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10

Quantitative Real-Time PCR Analysis

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Total RNAs were isolated using TRIzol reagent and reverse transcribed into cDNA with the qRT SuperMix (Vazyme). For real-time PCR, cDNA was amplified using a SYBR premix reagent on the CFX96 TouchTM Real-Time system (Bio-Rad). Rpl19 and GAPDH were used for normalization. Prl8a2 (previously called Dtprp), IGFBP1, and Caveolin-1 mRNA expression were analyzed. The primer sequences used for qPCR were listed in Table 1. Data from Real-Time PCR were analyzed using the 2−ΔΔCt method.
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