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Cf96 real time system

Manufactured by Bio-Rad
Sourced in United States

The CF96 Real-Time system is a thermal cycler designed for real-time PCR analysis. It features a 96-well format and supports a wide range of fluorescent chemistries for gene expression, genotyping, and other applications.

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6 protocols using cf96 real time system

1

Resveratrol-Loaded Hydrogel Attenuates Macrophage Inflammation

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The anti-inflammatory effect of resveratrol-loaded hydrogel was studied in vitro using lipopolysaccharide (LPS)-induced inflammation on RAW 264.7 macrophage cells. The peptide-hydrogels loaded with/without resveratrol were prepared on the bottom of a 6-well plate. Macrophage cells (1.0 × 106 cells) were added into wells, and LPS was added after 6-h incubation. After 24-h or 48-h treatment, cells were collected for qRT-PCR assay to detect the mRNA expression of inflammatory cytokines TNF-α and IL-1β. The procedures are as follows. Total RNA was extracted by Trizol, and then the cDNA was obtained by using reverse transcription kit (PrimeScript RT reagent Kit, Takara, China). The analysis was performed on the CF96-Real-Time System (Bio-rad, USA) using SYBR Green Premix Ex Taq II (Takara, Beijing, China). The housekeeping gene GAPDH was employed as a control gene. The primers for the target genes are listed in Table 1.
After 24-h or 48-h treatment, the culture medium was collected to detect the concentration of TNF-α and IL-1β secreted by macrophages using ELISA kit (R&D Systems, USA). The absorbance at 450 nm was measured using a microplate reader, and the concentrations were obtained by measuring the standard curves.
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2

Transcriptomic analysis of B. amyloliquefaciens

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Cell pellets (6 samples per strain) were used for isolating RNA with RNeasy Mini Kit, then mRNA was enriched with RiboZero rRNA Removal Kit (Qiagen, German). Library preparations for paired-end sequencing were performed on the Illumina HiSeq, and the obtained sequences were mapped onto the reference genome of B. amyloliquefaciens (NCBI Accession no: HE617159.1). To quantify gene transcription from the obtained sequence reads, RPKM values (Reads Per Kilobase per Million mapped reads) were calculated using the number of reads mapped to a gene, the total amount of mapped reads in the experiment, and the length in base pairs for a gene. The thresholds for significant changes in gene transcription were fold-changes of greater than 2 or less than 0.5 with p < 0.05 and 0.01, respectively (Kröber et al., 2016 (link)).
Some key genes transcription were quantified by Quantitative Real-Time PCR (qRT-PCR). RNA was extracted as above, then cDNA was produced by reverse transcription with 1 μg RNA, iScript Select cDNA Synthesis Kit and random oligonucleotide primers (Bio-Rad). qRT-PCR was performed with cDNA, SsoAdvanced Universal SYBR Green Supermix (Bio-Rad) and target-specific primers in CF96 Real-Time System (Bio-Rad). All expression data were normalized to the copy number of 16S rRNA in each sample.
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3

Aortic Expression Analysis of KDM5C and KDM6A

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RNA was extracted from the thoracic aorta (defined as the segment extending from the aortic root to the diaphragm) and abdominal aorta (defined as the segment extending from the diaphragm to the iliac bifurcation) from XXF and XOF Ldlr−/− mice fed a Western diet for 1 week. RNA was extracted using a Maxwell Rapid Sample Concentrator (RSC) simply RNA Tissue kit (REF#AS1340, Promega, Madison, WI). RNA (226 ng) was reverse transcribed to cDNA using Supermix (cat#95048-500, Quanta Biosciences, Gaithersburg, MD). cDNA was diluted (1:10) and mRNA abundance of Kdm5c or Kdm6a was quantified by RT-PCR using SYBER Green FastMix (cat#95071-012, Gaithersburg, MD) on a BioRad quantitative real-time PCR thermocycler (CF96 Real-Time system, BioRad, Hercules, CA). mRNA abundance was determined using the ΔΔCt method and normalized to β-actin as a housekeeping gene.
Primer sequences for Kdm5c were: Forward 5’-ACCCACCTGGCAAAAACATTGG-3’; reverse 5’-ACTGTCGAAGGGGGATGCTGTG-3’. Primers sequences for β-actin were: 5’-GCTCTGGCTCCTAGCACCAT-3’; reverse 5’-GCCACCGATCCACACAGAGT-3’. Primer sequences for Kdm6a were: Forward 5’-CCAATCCCCGCAGAGCTTACCT-3’; reverse 5’-TTGCTCGGAGCTGTTCCAAGTG-3’.
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4

Quantitative Expression Analysis of Coding and Non-Coding Genes

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The mRNA expression levels of candidate coding and non-coding genes were validated by qPCR, which was performed using SYBR Premix ExTaq (Tiangen Biotech, Beijing, China) on the CF96 real-time system (Bio-Rad, USA). The cDNA synthesis of coding genes was performed using Quantscript RT Kit Quant cDNA (Tiangen Biotech, Beijing, China) with approximately 300 ng of total RNA as the template. For lncRNA and miRNA, the lnRcute lncRNA First-Strand cDNA Kit (Tiangen Biotech, Beijing) and the TaqMan® MicroRNA Reverse Transcription Kit (Thermo Fisher Scientific, USA) were used, respectively. SYBR Premix ExTaq (Tiangen, Beijing, China) was used for real-time PCR, which is available for an ABI7500 Real-Time PCR system (Applied Biosystems). The Tm values for each reaction are listed in Additional file 2: Table S5. The miRNA primers were designed and purchased from RiboBio Co., Ltd. (Guangzhou, China). The β-actin gene was used as a reference gene, and U6 was used as the miRNA reference control. Each plate was repeated three times in independent runs for all the references. Gene expression was evaluated using the 2−∆∆Ct method [45 (link)].
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5

Quantitative RT-PCR Analysis of RR-TZF Genes

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RNA extraction and Real-time quantitative RT-PCR were conducted as described previously [71 (link)]. Total RNA was extracted from the samples using a TRIzol reagent kit (Invitrogen, Carlsbad, CA, US) according to the manufacturer’s specifications. The RNA integrity was evaluated using agarose gel electrophoresis and ethidium bromide staining. The RNA preparation was then treated with Dnase I and first strand synthesis of cDNA was performed by using oligo (dT) primer and RT Enzyme (Thermo Fisher, USA).
The quantitative real-time PCR was carried out with SYBR-green fluorescence using a CF × 96 Real Time System (BIORAD) with a 20 μl PCR reaction mixture that included 8.8 μl of diluted cDNA, 10 μl of 2 × FastStart Universal SYBR Green Master (ROX) (Roche, Switzerland), and 0.6 μl of forward and reverse primer (Additional file 9). The BraA02g003190 gene was used as a reference gene. Each sample was run in triplicate for analysis. At the end of the PCR cycles, melting curve analysis was performed to validate the specific generation of the expected PCR product. The expression levels of RR-TZF genes were calculated with the 2 − ΔΔCT method [78 (link)].
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6

Quantitative Assessment of Fungal Infection

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Leaf tissue collected for analysis was frozen in liquid nitrogen and stored at -70°C until use. Total RNA was extracted using TRIzol reagent (Invitrogen) following the manufacturer’s instructions. Total RNA was treated with DNase I and purified with NucleoSpin RNA II kit (Macherey-Nagel). RNA quantity was measured on a Nanodrop (ND-1000 spectrophotometer) from Thermo Scientific. We used Superscript VILO cDNA synthesis kit (Invitrogen) for cDNA synthesis following manufacturer’s instructions. After quantification and dilution, 100 ng of cDNA was used as the template for each RT-PCR reaction using SsoFast EvaGreen Supermix (Bio-Rad) on a Bio-Rad CF96 Real-Time system coupled to a C1000 Thermal Cycler (Bio-Rad). Target gene expression was normalized to actin.
For fungal DNA quantification, amplifications were conducted on an optical 96-well plate using the Mx3005P real-time PCR detection system (Stratagene) and SYBR Green master mix (Stratagene/Bio-Connect). M. oryzae 28S rDNA was assayed in triplicate using 25 ng as input DNA and a passive reference dye (ROX) according to the manufacturer’s instructions (Stratagene). Two pools of DNA for each line were tested for DNA quantification. Each pool consisted of the youngest fully developed leaf from six individual plants.
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