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Abi sequence detector software version 2

Manufactured by Thermo Fisher Scientific
Sourced in United States

The ABI Sequence Detector Software version 2.0 is a software application designed to analyze and interpret data generated by real-time PCR instruments. The software provides a user-friendly interface for setting up experiments, monitoring reactions, and analyzing results.

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6 protocols using abi sequence detector software version 2

1

Real-time RT-PCR analysis of melanogenic genes

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The real-time RT-PCR analysis was performed using an ABI7900HT Instrument (Applied Biosystems, Waltham, MA, USA). For the TaqMan analysis, predesigned or optimized assays on demand (Applied Biosystems) were used, including MITF (ID: Hs01117294_m1), tyrosinase (ID: Hs00165976_m1), TRP-1 (ID: Hs00167051_m1), TRP-2 (ID: Hs01098278_m1), glyceraldehyde-3-phosphate dehydrogenase (GAPDH) (ID: Hs00266705_g1), hypoxanthine-guanine phosphoribosyltransferase (HPRT) (Hs02800695_m1), and 18S (Hs03003631_g1). The data were analyzed using ABI Sequence Detector Software version 2.0 (Applied Biosystems). Total RNA was extracted from cells using TRI reagent® according to the manufacturer's instructions and stored at -70°C until use. cDNA was synthesized from total RNA (1 μg) using MuLV reverse transcriptase according to the manufacturer's instructions. The real-time RT-PCR analysis was conducted as previously described [20 (link)]. The results were normalized to the expression level of endogenous GAPDH and were also tested against two additional housekeeping genes (18S and HPRT). We found that the results were not significantly different from those obtained using GAPDH. Expression levels of the target genes were normalized to the levels observed in the controls. The results were verified by repeating each experiment four times in triplicate.
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2

Quantitative Real-Time RT-PCR Analysis

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Real-time RT-PCR analysis was performed using an ABI7900HT Instrument (Applied Biosystems, Waltham, MA, USA). For TaqMan analysis, predesigned or optimized assays on demand (Applied Biosystems) were used, including Nrf2 (ID: Hs00975961_g1), NQO1 (ID: Hs01045993_g1), AhR (ID: Hs00169233_m1), CYP1A1 (ID: Hs01054796_g1), glyceraldehyde-3-phosphate dehydrogenase (GAPDH) (ID: Hs00266705_g1), hypoxanthine-guanine phosphoribosyltransferase (HPRT) (Hs02800695_m1), and 18S (Hs03003631_g1). The data were analyzed using ABI Sequence Detector Software version 2.0 (Applied Biosystems). Total RNA was extracted from cells using TRI reagent® according to the manufacturer's instructions and stored at -70°C until use. cDNA was synthesized from total RNA (1 μg) using MuLV reverse transcriptase according to the manufacturer's instructions. Real-time RT-PCR analysis was conducted as previously described [18 (link)]. The results were normalized to the expression level of endogenous GAPDH and were also tested against two additional housekeeping genes (18S and HPRT). We found that the results were not significantly different from those obtained using GAPDH. Expression levels of target genes were normalized to the levels observed in controls. Results were verified through four-time repetition of the same experiment, each of which was conducted in triplicate.
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3

RT-PCR Analysis of Nrf2, CYP1A1, and HO-1

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Real-time polymerase chain reaction (RT-PCR) analysis was conducted as previously described [25 (link)]. Specifically, RT-PCR analysis was done with an ABI7900HT Instrument (Applied Biosystems, Waltham, MA, USA). Predesigned or optimized assays on demand (Applied Biosystems) were used for TaqMan analysis. They include Nrf2 (ID: Hs00975961_g1), CYP1A1 (ID: Hs01054796_g1), HO-1 (ID: Hs01110250_m1), glyceraldehyde-3-phosphate dehydrogenase (GAPDH) (ID: Hs00266705_g1), 18S (Hs03003631_g1), and hypoxanthine-guanine phosphoribosyltransferase (HPRT) (Hs02800695_m1). ABI Sequence Detector Software version 2.0 (Applied Biosystems, Waltham, MA, USA) was used to analyze the data. TRI reagent® was introduced to extract total RNA from the cells according to the manufacturer’s protocols and the total RNA was stored at –70 °C until use. MuLV reverse transcriptase was used to synthesize cDNA from the total RNA (1 μg) according to the manufacturer’s instructions. RT-PCR results was analyzed as previously reported [19 (link)]. The data were normalized to the expression level of three housekeeping genes such as GAPDH, 18S, and HPRT. The expression levels of target genes were normalized to the levels measured in the controls. The same experiment was repeated four times to verify the results and each experiment was conducted in triplicate.
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4

Real-Time RT-PCR Analysis of Gene Expression

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Real-time RT-PCR analysis was performed using an ABI7900HT Instrument (Applied Biosystems, Waltham, MA, USA). For TaqMan analysis, predesigned or optimized assays on demand (Applied Biosystems) were used, including EGFR (ID: Hs01076090_m1), TRPV1 (ID: Hs00949993_g1), glyceraldehyde-3-phosphate dehydrogenase (GAPDH) (ID: Hs00266705_g1), hypoxanthine-guanine phosphoribosyltransferase (HPRT) (Hs02800695_m1), and 18S (Hs03003631_g1). The data were analyzed using ABI Sequence Detector Software version 2.0 (Applied Biosystems). Total RNA was extracted from cells using the TRI reagent® according to the manufacturer's instructions and stored at -70°C until use. cDNA was synthesized from total RNA (1 μg) using MuLV reverse transcriptase according to the manufacturer's instructions. Real-time RT-PCR analysis was conducted as previously described [30 (link)]. The results were normalized to the expression level of endogenous GAPDH and were also tested against two additional housekeeping genes (18S and HPRT). We found that the results were not significantly different from those obtained using GAPDH. Expression levels of target genes were normalized to the levels observed in controls. Results were verified through four-time repetition of the same experiment, each of which was conducted in triplicate.
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5

Quantitative Analysis of Pluripotency Markers

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Real-time RT-PCR analysis was conducted using an ABI7900HT machine (Applied Biosystems). All TaqMan RT-PCR reagents, including primers and probes, were purchased from Applied Biosystems. TaqMan analysis was conducted using predesigned and optimized Assays on Demand (Applied Biosystems). The following assays were used: HIF-1α (ID: Hs00936371_m1), HIF-2α (ID: Hs01026149_m1), OCT4 (ID: Hs03005111_g1), NANOG (ID: Hs02387400_g1), SOX2 (ID: Hs01053049_s1), REX1 (ID: Hs01938187_s1), GAPDH (ID: Hs00266705_g1). The reaction parameters were as follows: 2-min 50°C hold, 30-min 60°C hold, and 5-min 95°C hold, followed by 45 cycles of 20-s 94°C melting and 1-min 60°C annealing/extension. All measurements were performed in duplicate or triplicate and the results were analyzed using the ABI sequence detector software, version 2.0 (Applied Biosystems). Relative quantitation was conducted using GAPDH as a reference gene, which was validated using the NormFinder software (supporting information in S1 Fig and S1 Table). Since all assays used were optimized for PCR efficiency by the manufacturer, mRNA expression levels were estimated by the delta ct values.
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6

Gene Expression Analysis in Melanocytes

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TRIzol reagent (ThermoFisher Scientific, Waltham, MA, USA) and moloney murine leukemia virus reverse transcriptase (ThermoFisher Scientific) were used to extract total RNA from cells and synthesize cDNA, respectively. An ABI7900HT Real-time PCR Instrument (Applied Biosystems, Waltham, MA, USA) was introduced for real-time RT-PCR analysis. The real-time RT-PCR analysis was conducted using TaqMan probes (Applied Biosystems) including Tyrosinase (ID: Mm00495818_m1), MITF (ID: Mm01182484_m1), TRP-1 (ID: Mm01268471_m1), TRP-2 (ID: Mm01225584_m1), hypoxanthine-guanine phosphoribosyltransferase (HPRT) (Mm00446966_m1), 18S (Mm04277571_s1), and GAPDH (ID: Mm99999915_g1). The PCR reaction was done with parameters as follows: 50 °C for 2 min, 60 °C for 30 min, and 95 °C for 5 min, and then 45 cycles of 94 °C for 20 s and 60 °C for 1 min as described previously36 (link). The PCR results were normalized to the expression level of three housekeeping genes (GAPDH, 18S and HPRT) using ABI sequence detector software version 2.0 (Applied Biosystems). Results were confirmed from at least three independent experiments.
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