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Light cycler sybr green 1 master

Manufactured by Roche
Sourced in Switzerland, Germany, United States

The Light Cycler SYBR Green I Master is a real-time PCR reagent kit designed for gene expression analysis and quantification. It contains all the necessary components for performing SYBR Green-based real-time PCR reactions, including the SYBR Green I dye, DNA polymerase, and reaction buffer.

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29 protocols using light cycler sybr green 1 master

1

Macrophage Polarization Dynamics

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After washing, adherent macrophages were immediately stimulated with IFNγ (40 UI ml−1, Clinisciences), IL-6 (50 ng ml−1, Clinisciences), LPS (1 ng ml−1, Sigma), IL-4 (50 ng ml−1, Miltenyi Biotech), IL-13 (50 ng ml−1, Clinisciences), IL-10 (50 ng ml−1, Clinisciences), 15-HETE (1 μM, Cayman) or DLPC (50 μM, Sigma) for 4 or 24 h. In indicated experiments, adherent macrophages were pre-incubated or not with a Jak-2/STAT6 inhibitor, AG490 (1 nM, Tebu-Bio).
The mRNA preparation was made using the EZ-10 Spin Column Total RNA Minipreps Super Kit (Bio Basic) using the manufacturer's protocol. Synthesis of cDNA was performed according to the manufacturer's recommendations (Thermo electron). RT–qPCR was performed on a LightCycler 480 system using LightCycler SYBR Green I Master (Roche Diagnostics). The primers (Eurogentec) were designed with the software Primer 3. Actb (Actin) mRNA was used as the invariant control. Serially diluted samples of pooled cDNA were used as external standards in each run for the quantification. Primer sequences are listed in Supplementary Table 1.
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2

Quantitative Gene Expression Analysis

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Total RNA was extracted using RNAprep pure MicroKit (Aidlab, Beijing, China) following the manufacturer’s instructions. cDNA was synthesized by using cDNA Synthesis Kit (TaKaRa, Dalian, China). Reverse transcription parameters were set as follows: 42 °C for 50 min and 65 °C for 15 min. For PCR, the primers were listed in table 1. PCR amplification was carried out on a Light Cycler real-time PCR instrument (Roche, Mannheim, Germany). The amplification procedure was conducted according to manufacturer’s instructions using a Light Cycler SYBR Green I Master (Roche). The PCR parameter were set at 95 °C for 10 min, followed by 55 cycles at 95 °C for 10 s, 60 °C for 30 s, and finally cooling at 4 °C.
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3

Quantitative gene expression analysis

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Total RNA was extracted from cell aggregates using SPARKeasy Tissue/Cell RNA Rapid Extraction Kit (SPARKjade, AC0202, Shandong, China) and reverse transcription was performed using a SPARKScript RT plus Kit (SPARKjade, AG0304). A Light Cycler SYBR Green I Master (Roche, 04707516001, Mannheim, Germany) kit was used to prepare PCR mix and PCR was performed using a Light Cycler 480 Real-Time PCR System (Roche, Mannheim, Germany). The relative gene expression was calculated using the 2−(△△Ct) method and Gaphd was used as a housekeeping gene. Primer sequences used are listed in Additional file 2: Table S2.
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4

Quantitative Analysis of RANKL and OPG Expression in Gingival Tissues

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Animals were euthanized by CO2 inhalation and the maxilla was removed from each mice. Gingival tissues around the first molars were isolated under a surgical microscope and were immediately homogenized using Homogenizing Kit (OMMNI). Totally RNA was extracted using PureLink® RNA Mini Kit (Ambion) and were reversed transcribed using the SuperScript II Reversed Transcriptase kit (Invitrogen). Predesigned primers of RANKL, OPG and GAPDH were from Sigma. The respective primer sequences are as follows: RANKL: TGTACTTTCGAGCGCAGATG and AGGCTTGTTTCATCCTCCTG; OPG: AGCAGGAGTGCAACCGCACC and TTCCAGCTTGCACCACGCCG; GAPDH: CCCCAGCAAGGACACTGAGCAA and GTGGGTGCAGCGAACTTTATTGATG. Quantitative PCR was conducted using the LightCycler® SYBR Green I master and LightCycler® 480 Instrument system (Roche).
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5

Quantifying Oral Bacterial Burden

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On Day 0 and Day 20, oral swabs were taken from around molar teeth and periodontal gingival surface (after the removal of close coil spring appliance on Day 20) from each mouse. Samples were resolved in 200µl of PBS and DNA was extracted from each sample as previously described (19 (link)) and was quantitated by real-time PCR (RT-PCR) using the LightCycler® SYBR Green I master and LightCycler® 480 Instrument system (Roche). A universal 16S rRNA gene primer was used to quantitate the total oral bacteria recovered from each animal: 5’-GAGTTTGATYMTGGCTCAG and 5’-AAGGAGGTGWTCCARCC-3’. The quantity of total bacterial DNA from each sample was extrapolated from the DNA standard curve derived from serial dilution of E. coli bacteria with known concentrations. Each experiment was carried out in duplicate and the data were obtained from all animals in each group (n=8).
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6

Quantification of mRNA Levels by RT-qPCR

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Messenger RNA (mRNA) was isolated using the RNAqueous-Micro Total RNA Isolation Kit (Thermo Fisher) following the manufacturer’s protocol and complementary DNA (cDNA) was synthesized according to the manufacturer’s recommendations (Verso Kit, Thermo Electron). Real-time quantitative polymerase chain reaction (RT-qPCR) was performed in a total volume of 10 μL with 60 cycles of 10 s at 95°C, 10 s at 60°C and 10 s at 72°C using a LightCycler 480 system and LightCycler SYBR Green I Master (Roche Diagnostics). The primers (at a final concentration of 5 µM) were designed with the software Primer 3. The glyceraldehyde-3-phosphate dehydrogenase (Gapdh) mRNA was used as the invariant control. Serially diluted samples of pooled cDNA were used as external standards in each run for the quantification. Primer sequences are listed in online supplemental table 1.
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7

Validating RNA-seq Data by RT-qPCR

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The same experimental setup used for RNA-seq data generation was followed for experimental validation by RT-qPCR including infections with Pto AvrRpt2 , Pto AvrRps4, Pto hrpC-and Pto EV. Briefly, tissue was snap frozen and RNA isolated with the Maxwell® RSC Plant RNA kit (Promega). 1 µg of RNA was reverse transcribed into cDNA with the High-Capacity cDNA Reverse Transcription Kit with RNase inhibitor (Applied Biosystems TM ). RT-qPCRs were performed with LightCycler® SYBRgreen I master (Roche) in a LightCycler® 480 System (Roche). Data was analyzed using the ΔΔCT method and represented as fold enrichment of the time point tested (4 or 6 hpi) relative to 0 hpi. Primers for RT-qPCR used in this study are listed in Table S1.
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8

Quantitative Real-Time PCR Analysis

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PCR amplification and analysis were performed on a Light Cycler 96 instrument (Roche, Mannheim, Germany). All reactions were performed using LightCycler SYBR Green I master (Roche), according to the manufacturer's instruction. The following primers were used: RANK sense 5′-ACCAGCATCAAAATCCCAAG-3′, antisense 5′-CCCCAAAGTATGTTGCATCC-3′; matrix metalloproteinase 9 (MMP9) sense 5′-TGGGGGGCAACTCGGC-3′, antisense 5′-GGAATGATCTAAGCCCAG-3′; cathepsin K sense 5′-TGAGGCTTCTCTTGGTGTCCATAC-3′, antisense 5′-AAAGGGTGTCATTACTGCGGG-3′; β-actin sense 5′-GGACTTCGAGCAAGAGATGG-3′, antisense 5′-TGTGTTGGGGTACAGGTCTTTG-3′. mRNA expression levels were normalized to that of β-actin.
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9

Quantifying Gingival Gene Expression

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Palatal gingival tissues were isolated from around ligatured implants and were homogenized in lysis buffer using a tissue homogenizer. Total RNA was extracted using PureLink® RNA Mini Kit (Ambion). cDNA was synthesized using the SuperScript III Reversed Transcriptase kit (Invitrogen) according to the manufacturer’s protocol. The mRNA expression of TNF-α and RANKL in gingival was determined by real-time quantitative PCR (RT-qPCR) using LightCycler® SYBR Green I master and LightCycler® 480 Instrument system (Roche). GAPDH gene was used as an internal control. The sequences of primers are listed as follows: TNF-α forward 5′-CACAGAAAGCATGATCCGCGACGT-3′; TNF-α reverse 5′-CGGCAGAGAGGAGGTTGACTTTCT-3′; RANKL forward 5′-GGGTGTGTACAAGACCC-3′; RANKL reverse 5′-CATGTGCCACTGAGAACCTTGAA-3″ GAPDH forward 5′-CCCCAGCAAGGACACTGAGCAA-3′; GAPDH reverse 5′-GTGGGTGCAGCGAACTTTATTGATG-3′.
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10

Antioxidant Gene Expression in Granulosa Cells

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After anthocyanin and/or Rosup treatments, the cells were collected with trypsinization. The mRNA expression of superoxide dismutase (SOD1), catalase (CAT) and glutathione peroxidase (GPX1) in the cells was analyzed by qRT-PCR. Primer3 was used for primers design in this study (Table 1). Total RNA of GCs was extracted using an RNA extraction kit (Aidlab, Beijing, China) according to the manufacturer’s protocols. Total RNA was reverse transcribed to cDNA (Takara, Dalian, China) and gene expression was quantified by real time RT-PCR (LightCycler 480 Real-time PCR System, Germany) using a Light Cycler SYBR Green I Master (Roche, Dalian, China). The reaction system contained 2 μL cDNA, 10 μL SYBR green master mix, 0.4 μL each of primers (10 μM) and 7.2 μL RNase free dH2O. Gene expression is presented as 2−ΔΔCt. Relative fold changes were calculated and compared to controls (n≥3).
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