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5 protocols using lightcycler 1536

1

Real-Time qPCR Analysis of Gene Expression

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Total RNA was extracted from RET WAT with Rneasy lipid tissue mini kit from Qiagen. RNA was quantified by spectrophotometric Nanodrop. Total RNA (500ng) was reverse transcribed using SuperScript® III First-Strand Synthesis SuperMix kit from Life Technologies. Samples of cDNA were diluted 1:40, amplified and used for RT-qPCR measurements using SYBR Green from Roche as previously described.14 (link) RT–qPCR was performed in the LightCycler1536 instrument from Roche as follows: 75°C for 2min, 95°C for 10min, 40 cycles of denaturation (95°C for 15s to the denaturation, 60°C for 30s to the annealing, 72°C for 30s to the extension). Results were analyzed with the LightCycler1536 software from Roche. Ribosomal RPL13 RNA was used to normalize cDNA. Quantification of mRNA was carried out by comparing the number of cycles required to reach reference and target threshold values (2^-(δ−δ Ct) method) as described previously.43 (link) Sequences of the rat sense and antisense nucleotides were: PGC1-α : 5′-tgcccctgccagtcacagga-3′ 5′-gctcagccgaggacacgagg-3′; PPARα : 5′-aagccatcttcacgatgctg-3′ 5′-tcagaggtccctgaacagtg-3′ ; PPARγ2 : 5′- ttatgctgttatgggtgaaa-3′ 5′- caaaggaatgggagtgtc-3′ ; TFAM : 5′-gttccggggaatgtggggcg-3′ 5′-gacaggcgagggtatgcggc-3′ ; UCP1 : 5′-tacagagttatagccaccaca-3′ 5′-tggaacgtcatcatgtttgtg-3′ ; RPL13 : 5′-tggcaggggcttcag-3′ 5′-tgggcatcacaggtcc-3′
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2

Chemokine and Angiogenesis Profiling of Sorted Cells

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Changes in chemokines and receptors or angiogenesis levels were measured with an RT2 Profiler PCR Array for mouse chemokines and receptors PAMM-022ZA or mouse angiogenesis PAMM-024ZR (Qiagen, Hilden, Germany). Total RNA was extracted from sorted eGFP+ cells from BM. The expression of 86 cytokine and chemokine genes was analysed with the LightCycler 1536 system (Roche Diagnostics, Mannheim, Germany), according to the manufacturer's instructions. The data obtained were analysed with the RT2 Profiler PCR Array Data Analysis Template (Qiagen). Data were normalized against five housekeeping genes (Actb, B2m, Gapdh, Gusb, Hsp90ab1), and relative expression levels were calculated by the 2−ΔΔCt method.
PCR array analyses were performed at the Hopital La Pitié Salpétrière ICM, with a LightCycler 1536 (Roche) and RT2 Profiler PCR Arrays.
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3

High-Throughput Real-Time PCR for Pathogen Detection

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A LightCycler® 1536 (Roche, Meylan, France) was used to perform high throughput real-time PCR amplifications as described previously (Delannoy et al., 2012a (link)), except that 1 μl of sample DNA was used in each reaction for a final reaction volume of 2 μl. The thermal profile was modified as follows: 95°C for 1 min, followed by 45 cycles of 95°C for 0 s, and 58°C for 30 s. All ramp rates were set to 2°C/s. E. coli gene targets used for the real-time PCR amplification and all primers and probes that have previously been described are reported in Table 2. An inhibition control (IC) was performed on each sample to check for potential inhibition of the PCR reaction due to intrinsic characteristics of the sample. The IC is a recombinant pBluescript IISK+ plasmid containing the dsb gene from Ehrlichia canis (Michelet et al., 2014 (link)). The plasmid was added to each sample at a concentration of approximately 0.3 pg/μl. Primers and probe specific for the E. canis dsb gene were used to detect the IC (Michelet et al., 2014 (link)).
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4

Quantitative PCR Analysis of Gene Expression

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Total RNA was extracted using the RNeasy Kit (Qiagen) per manufacturer’s instructions, and 1 μg of RNA was used for cDNA synthesis. 25–50 ng of the cDNA was used to perform expression analyses with Taqman on the StepOnePlus System (Applied Biosystems) or using the ViiA 7 Real-Time PCR System (Life Technology) and using SYBR Green on the LightCycler 1536 (Roche). All data were analyzed using Qbase+ software (Biogazelle). Quantitative PCR (qPCR) primers used for the analysis were purchased from Applied Biosystems or Primer Design. A set of 12 candidate reference genes (Primer Design) was tested, and the most stably expressed genes were determined using the geNorm tool of the Qbase+ software. These were used as reference to establish individual gene expression values (2−ΔΔCT). Four to five biological replicates (individual mice) for each genotype were analyzed in duplicate, and all samples were run on the same plate to avoid inter-run variation and calibration. qPCR analyses were performed in Portsmouth, Rouen, and Pittsburgh, and results for overlapping transcripts were cross-referenced between collaborating centers.
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5

Time-Course PHO5 Nucleosome Scanning

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PHO5 nucleosome scanning assay time-course was adapted from (Small et al., 2014 (link)) (Figure 6E). Isogenic strains (yDT197 – >WT, yDT180 –>hH3.1-core, yDT186 –> hH3.3-core) as indicated, were grown as two biological replicates in 50 ml SC medium (containing phosphate) with 2% glucose to an A600 of 1–1.3. Cultures were washed twice with 50 ml water to remove residual phosphate. To induce remodeling at the PHO5 promoter, cultures were then re-suspended in 60 ml SC medium without phosphate (Yeast Nitrogen Broth w/o phosphate (MP biomedicals, sku 114027812), 100 mg/L NaCl, amino acids, and glucose) to an A600 of 1, and then incubated at 30°C with shaking. Time points as indicated were treated as “MNase digestions” as described earlier except in a 10-fold reduced scale (e.g., 10 ml culture, 400 μl spheroblasting media, etc). Time-point cultures (10 ml) were normalized to an A600 of 1 for each time point. Processed MNase digested DNA was analyzed by qPCR using primers listed in Table S7 in a Roche LightCycler 1536 real-time PCR machine using LightCycler 1536 DNA Green Master (Roche) in technical triplicate.
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