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3 protocols using power sybr green 2 mastermix

1

Quantifying Gene Expression in Adipocytes and Macrophages

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At 12 hr, cells were washed with 1× PBS (Sigma, USA), lysed using a RNeasy kit (Qiagen, Canada) and processed according to the manufacturer's instructions. Only adipocytes and macrophages from the trans-well system were lysed because cells could be isolated separately in this system. cDNA was made from 1 µg of extracted RNA using a high capacity cDNA reverse transcription kit as per the manufacturer's instructions (Applied Biosystems, USA). Real-time PCR analysis was performed using a 7900HT Fast Real Time PCR system (Applied Biosystems, USA) using the default protocol:2 min at 50°C, 10 min at 95°C, 15 s at 95°C, 60°C for 1 min, 15 s at 95°C and 15 s at 60°C for a total of 40 cycles. Primers were designed using the Universal Probe Library Assay Design Center (Roche Applied Sciences, Germany, Table 1) and validated primer efficiencies were between 90–105%. Samples were run in triplicate in 96-well plates, and each 20 µL reaction contained 5 µL cDNA (50 ng), 0.4 µL of 10 µM primer solution, 10 µL Power Sybr green 2× master mix (Applied Biosystems, USA), and 4.6 µL of RNase free water. All results were normalized to Rplp0 mRNA expression, and the relative differences in gene expression between treatment groups and the pre-treatment (0 hr) were determined using the ΔΔCt method.
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2

Quantitative Analysis of White Adipose Tissue

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White adipose tissue (WAT) was collected at the week 18 necropsy from the intra-abdominal perigonadal depots. Tissue from the four heaviest animals in each treatment group was selected to capture the effects in animals most sensitive to weight gain. A range in sensitivity was expected due to the genetic variation in the outbred CD-1 mice used in the study. RNA was isolated by homogenizing WAT with an automated ceramic bead homogenizer FastPrep-24 5G (MP Biomedicals, Irvine, CA) in Trizol (Thermofisher Scientific, PA, USA) for 2 cycles of 4 m/s for 30sec. RNA was purified using a Qiagen RNeasy kit (Qiagen, MD, USA) and genomic DNA was removed using on-the-column DNase I digestion (Qiagen, MD, USA) and quantified with Nanodrop 2000 spectrophotometer (ThermoFisher Scientific, PA, USA). RNA (1 mg) was transcribed into cDNA using a High-Capacity cDNA Reverse Transcription Kit (Applied Biosystems, USA). cDNA (25 ng) was amplified in triplicate using a QuantStudio 7 Flex Real Time PCR System (Applied Biosystems) and Power SYBR Green 2 × Mastermix (Applied Biosystems, Foster City, Canada). Primer sets for all genes were pre-designed assays (IDT DNA, Redwood City, CA, USA) and are shown in Table S2. Mean Ct values were normalized to Rpl19 (60S ribosomal protein L19; housekeeping gene) and relative fold change mRNA levels were calculated by using ΔΔ CT method [43 ].
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3

Quantitative Analysis of White Adipose Tissue

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White adipose tissue (WAT) was collected at the week 18 necropsy from the intra-abdominal perigonadal depots. Tissue from the four heaviest animals in each treatment group was selected to capture the effects in animals most sensitive to weight gain. A range in sensitivity was expected due to the genetic variation in the outbred CD-1 mice used in the study. RNA was isolated by homogenizing WAT with an automated ceramic bead homogenizer FastPrep-24 5G (MP Biomedicals, Irvine, CA) in Trizol (Thermofisher Scientific, PA, USA) for 2 cycles of 4 m/s for 30sec. RNA was purified using a Qiagen RNeasy kit (Qiagen, MD, USA) and genomic DNA was removed using on-the-column DNase I digestion (Qiagen, MD, USA) and quantified with Nanodrop 2000 spectrophotometer (ThermoFisher Scientific, PA, USA). RNA (1 mg) was transcribed into cDNA using a High-Capacity cDNA Reverse Transcription Kit (Applied Biosystems, USA). cDNA (25 ng) was amplified in triplicate using a QuantStudio 7 Flex Real Time PCR System (Applied Biosystems) and Power SYBR Green 2 × Mastermix (Applied Biosystems, Foster City, Canada). Primer sets for all genes were pre-designed assays (IDT DNA, Redwood City, CA, USA) and are shown in Table S2. Mean Ct values were normalized to Rpl19 (60S ribosomal protein L19; housekeeping gene) and relative fold change mRNA levels were calculated by using ΔΔ CT method [43 ].
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