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10 protocols using lightcycler 96 qrt pcr system

1

Gene Expression Analysis by qRT-PCR

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The isolation of total RNA was performed using TRIzol reagent and treated with RNase‐free DNase. Then, we conducted reverse transcription and determined which RNA purity and concentration through the NanoDrop 2000C Spectrophotometer (Thermo Fisher Scientific, USA). qRT‐PCR analysis was conducted in technical triplicate in a Roche LightCycler®96 qRT‐PCR system (Roche, Germany). The internal control gene was. The comparative Ct method was used to determine the relative levels of target mRNA. The procedures of qRT‐PCR experiments as follows: 30 s at 95°C, followed by 40 cycles of 5 s at 95°C and 30 s at 60°C. For qRT‐PCR assay, primers of target genes were used as listed in Table 1.
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2

Quantitative Analysis of Lactobacillus plantarum Gene Expression

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L. plantarum and the derivate strains in the exponential growth period were collected by centrifugation at 4 °C. The total RNA was prepared and analyzed by qPCR as previously described [8 (link)]. The primers used for RT-PCR were listed in Table 6. Each PCR condition was performed in triplicate on the LightCycler 96 qRT-PCR system (Roche Diagnostics, Switzerland). The PCR procedure was as follows: 95 °C for 5 s, followed by 40 cycles of denaturation at 95 °C for 5 s and annealing at 60 °C for 30 s. 16S rRNA was used as the internal control. The obtained data was analyzed using analytical LightCycler 96 system, and the 2−ΔΔct method was used to calculate the transcriptional fold changes.

Primers used in qRT-PCR

PrimersSequence (5′–3′)
0057-qPCR-sACTTTGGTCCCAGAACG
0057-qPCR-aGACGAGCGATGATAGGC
P0202-qPCR-sTGTTTGCGATTTGATTG
P0202-qPCR-aGCCATACTTGCGTTCCT
P0203-qPCR-sGAGCGTTTAATAGTGTTC
P0203-qPCR-aTTAGCAAGCCCGTCATC
3533-qPCR-sACGGTACGATTTGCTTG
3533-qPCR-aCTGCGATGAACATTGAGA
3151-qPCR-sACAAGGGAAAGCTGATC
3151-qPCR-aAGCACTGTTAGCCGTAA
2768-qPCR-sCTTGCTTTGCCTTGTCC
2768-qPCR-aGTTGCCGTAAATAAGTTGAT
3153-qPCR-sGCCATTCAAGATTACGA
3153-qPCR-aTGATAGGTGCAGATAAGG
1745-qPCR-sCGCTGGTTGCAGGAATA
1745-qPCR-aGCACCGAACGGAGTAAG
0302-qPCR-sATTAAGCCAAATGCAATCAC
0302-qPCR-aAAACCATAGGCACCAGA
2920-qPCR-sCACTGCTTGTCGGGTTA
2920-qPCR-aATGGGAATGTTGCTTGAT
qPCR-16S-FCACATTGGGACTGAGACACGG
qPCR-16S-RCGATGCACTTCTTCGGTTGAG
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3

Validating High-Throughput Sequencing with qRT-PCR

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To verify the accuracy of the data obtained by high-throughput sequencing, four lncRNAs were randomly selected, and the results were confirmed by qRT-PCR for nine randomly selected lncRNAs. The RNAs were reverse transcribed into cDNA with HiScript II Q RT SuperMix for qRT-PCR (+gDNA wiper) (Vazyme, Nanjing, China). qRT-PCR was performed on a LightCycler® 96 qRT-PCR system (Roche, Basel, Switzerland) with ChamQ Universal SYBR qPCR Master Mix (Vazyme Biotech, Nanjing, China). β-actin were used as internal reference genes for mRNA. The relative expression levels were analyzed with the 2−ΔΔCt method. Experiments were repeated at least three times, and all data are presented as the mean ± standard error of the mean. Data were analyzed and plotted with Prism software (GraphPad, San Diego, CA, United States). The qRT-PCR primer sequences are listed in Supplementary Table S1.
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4

RNA Extraction and qRT-PCR Analysis

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RNA isolation and qRT-PCR were previously well described.11 (link)–16 (link) Briefly, total RNA was extracted from cells or fresh tissue specimens using Trizol Reagent (TaKaRa, Dalian, China) according to the manufacturer’s instruction. Then, mRNA was reversely transcribed to cDNA using the PrimeScript RT reagent Kit (TaKaRa). To evaluate the mRNA levels of a number of genes, qRT-PCR was performed on LightCycler® 96 qRT-PCR system (Roche, Switzerland) using SYBR Premix Ex Taq (Takara). GAPDH was used as the internal control. GAPDH forward primer: 5′-ACCCAGAAGACTGTGGATGG-3′, and GAPDH reverse primer: 5′-TCTAGACGGCAGGTCAGGTC-3′; Cirbp forward primer: 5′-AGGGCTGA GTTTTGACACCAA-3′, and Cirbp reverse primer: 5′-ACAAACCCAAATCCCCGAGAT-3′; E-cadherin forward primer: 5′- ATTTTTCCCTCGACACCCGAT-3′, and E-cadherin reverse primer: 5′-TCCCAGGCGTAGACCAAGA-3′; Ki67 forward primer: 5′- TATCAAAAGGAGCGGGGTCG-3′, and Ki67 reverse primer: 5′- TTTCATACCTTCCAAACAAGCAG-3′. All samples were normalized to internal controls and fold changes were calculated based on relative quantification (2−△△Ct).
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5

Quantifying Gene Expression Changes

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The total RNA was isolated from the cells by using TRIzol reagent, as per the manufacturer’s instructions. Moreover, the RNA samples were treated with RNase-free DNase and subjected to reverse transcription with PrimerScript RT Reagent Kit. The NanoDrop 2000C Spectrophotometer (Thermo Fisher Scientific, USA) was used to detect the RNA purity and concentration of each sample, while a qRT-PCR analysis was performed in technical triplicate using the TB Green qRT-PCR kit with a Roche LightCycler 96 qRT-PCR system (Roche, Germany). All the data were generated using cDNA from triplicate wells for each condition. Furthermore, the comparative CT method was used to calculate the relative quantity of the target gene messenger RNA (mRNA), and GAPDH gene was used as the internal control. The following procedure was followed for the qRT-PCR experiments: 30 s at 95°C, followed by 40 cycles of 5 s at 95°C and 30 s at 60°C. PCR analysis was performed with human primer sets (forward and reverse, respectively) for Rictor: F’- CGAGTACGAGGGCGGAAT, R’- ATCTGGCCACATTTTGGAGA; HMOX1: F’-TGCTCAACATCCAGCTCTTTGA, R’- AACTGTCGCCACCAGAAAGC; GAPDH: F’- CAACGAATTTGGCTACAGCA, R’- AGGGGTCTACATGGCAACTG.
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6

RNA Isolation and qRT-PCR Analysis

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TRIzol reagents were used to isolate total RNA. RNase-free Dnase was added to remove DNA. The RNA was then reverse transcribed. Sequentially, qRT-PCR analysis was conducted in technical triplicate in a Roche LightCycler®96 qRT-PCR system (Roche, Penzberg, Germany) to determine the relative levels of target mRNA [33 (link)]. The primers of the target genes used are listed in Table 1.
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7

Quantitative Gene Expression Analysis

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Total RNA was extracted from cells using TRIzol reagent (Vazyme, China), and quantitative determination of RNA concentration was performed by spectrophotometry (Thermo, Waltham, MA, USA). Total RNA was reverse transcribed into cDNA using HiScript II Q RT SuperMix for qRT–PCR (+ gDNA wiper) (Vazyme, Nanjing, China). qRT–PCR was performed on a LightCycler® 96 qRT–PCR system (Roche, Basel, Switzerland) with ChamQ Universal SYBR qPCR Master Mix (Vazyme Biotech, Nanjing, China). β-actin was used as an internal reference gene for mRNA, and U6 was used as the internal reference gene for miRNA. The relative expression levels were analyzed with the 2−ΔΔCt method. The experiments were performed with a minimum of three technical replicates, and all data are presented as the mean ± standard error of the mean. The primer sequences are listed in Table S2.
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8

Quantifying IRF6 Expression in Ovarian Cancer

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Human ovarian cancer tissues and adjacent noncancerous tissues were collected, and total RNA was extracted using TRIzol Reagent (Invitrogen) according to the kit instructions. 1 μg of total RNA was reverse‐transcribed to cDNA using the cDNA Reverse Transcription kit (Vazyme, Nanjing, China) at 37 °C for 60 min. Real-time PCR was performed using TB Green™ Premix Ex Taq™ II (RR420A; Takara, China) in a Roche LightCycler®96 qRT-PCR system according to the manufacturer’s protocol. Primers for IRF6 (interferon regulatory factor 6) were, forward: 5′- CCCCAGGCACCTATACAGC-3′ and reverse: 5′- TCCTTCCCACGGTACTGAAAC-3′; GAPDH was used as an internal reference for the calculation of IRF6 RNA expression, expression difference was calculated using 2−ΔΔCT method.
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9

Quantitative RT-PCR Protocol for Gene Expression

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Total RNA was isolated using TRIzol (Invitrogen), and complementary DNA was synthesized from 1 μg of RNA using the PrimeScript RT Reagent (Takara, Japan) following the manufacturer's instructions. The quantitative RT-PCR (qRT-PCR) was performed using FastStart Universal SYBR Green Master (Yeasen, China) in a Roche LightCycler 96 qRT-PCR System. The mRNA expression values were normalized to that of the ACTB gene. The primer sequences were listed in Table 1.
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10

Gene Expression Analysis via qRT-PCR

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The total RNA was extracted from the tissue and CPMs using TRIzol reagent (TaKaRa, Tokyo, Japan). The RNA concentration was quantified using a spectrophotometer (Thermo, Waltham, MA). cDNA was synthesized by reverse transcription using a PrimeScript RT reagent kit with gDNA eraser (TaKaRa, Japan). MiRNA was reverse transcribed using a ReverTra Ace qPCR RT kit (Toyobo, Tokyo, Japan). Then, qRT-PCR was performed using SYBR Green master mix (TaKaRa, Tokyo, Japan). The qRT-PCR reactions were performed using a LightCycler 96 qRT-PCR system (Roche, Basel, Switzerland). GAPDH was used as internal reference gene for mRNA, and U6 was used as an internal reference for miRNA. All experiments were performed in triplicate. The relative quantification of genes was performed using the 2−ΔΔCt method (Bubner and Baldwin, 2004 (link)). The BμLge-Loop miRNA qRT-PCR-specific primers, mimics, and inhibitors were designed by RiboBio (RiboBio, Guangzhou, China). The primer sequences are listed in Table S1.
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