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5 protocols using universal probe library probe

1

Quantitative Real-Time PCR Protocol

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NucleoZOL (Macherey‐Nagel) was used to perform total RNA extraction according to the manufacturer's recommendations. The First‐Strand cDNA Synthesis Kit (GE Healthcare, Chalfont St Giles, UK) was used to synthesize cDNA from 2 μg of total RNA, according to the manufacturer's instructions. The RT reaction mixture was diluted 1:4 and used as a cDNA template for qPCR. TaqMan quantitative PCR was carried out on a FX96 Thermocycler (Bio‐Rad). The PCR mixture contained TaqMan mix (Roche), 200 nM of primers (see Table S2 for their sequence), Universal Probe Library probe (100 μM, ThermoFisher Scientific) for the gene of interest (TaqMan Gene Expression Assays [Primers/probe], Life technologies), and 50 ng/μg of cDNA template. Reactions were performed in triplicate with the following program: 95°C 10 min, followed with 40 cycles of 95°C for 10 s, 59°C for 30 s. The relative amount of mRNA was calculated using the comparative Ct (ΔΔCT) method, following data normalization against GAPDH housekeeping gene.
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2

Real-Time qPCR Analysis of Gene Expression

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Total RNAs were extracted using NucleoZOL (Macherey-Nagel) according to the manufacturer’s instructions. RNAs were reverse transcribed with First-Strand cDNA Synthesis Kit (GE Healthcare) following the manufacturer’s recommendations. TaqMan real-time quantitative PCR was then run with PCR mixture containing TaqMan mix (Roche), 200 nM of primers, Universal Probe Library probe (100 µM, ThermoFisher Scientific), and cDNA template. Reactions were performed in triplicate on a FX96 Thermocycler (Bio-Rad). The comparative Ct (ΔΔCT) method and normalization with GAPDH housekeeping gene were used to calculate the relative amount of mRNA. Sequences of primers are as follows: CALB1:Sens 5′-aagatccgttcggtacagctt-3′, Anti-sens 5′-ctgaaggatctgtgcgagaa-3′; CALB2:Sens 5′-tcatttcctttttgtttttctcg-3′, Anti-sens 5′-gcgatcttcacattttacgaca-3′; NFATc1: Sens 5′-ggtcagttttcgcttccatc-3′, Anti-sens 5′-ccaaggtcattttcgtggag-3′; GAPDH: Sens 5′-agccacatcgctcagacac-3′, Anti-sens 5′-gcccaatacgaccaaatcc-3′.
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3

Quantitative PCR Protocol Using TaqMan Assays

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RNA was prepared using an RNeasy Mini Kit (Qiagen) and DNAse I (Qiagen) and retrotranscribed with SuperScript III (Thermo Fisher Scientific) and random hexamers (Thermo Fisher Scientific). Quantitative PCR was performed with Universal Probe Library assays (Roche). Reactions were carried out in duplicate in a QuantStudio 12K Flex (Applied Biosystems) with 1× TaqMan Fast Advanced Master Mix (Thermo Fisher Scientific), 1 µM forward and reverse primers and 250 nM Universal Probe Library probe, or 1× TaqMan assay. Quantification was performed using standard curves, with duplicate means reported, normalized by TBP or RPLP0, as indicated. Oligonucleotides are listed in Supplementary Table 5.
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4

Quantitative PCR for Gene Expression

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Total RNAs were extracted with phenol-chloroform using Upzol (Dutscher, Brumath, France). Synthesis of cDNA was performed using Maxima First cDNA Synthesis Kit (ThermoFisher Scientific) from 1 μg of total RNA. cDNA (50 ng/µL) was used as a template for quantitative PCR (qPCR), and mixed with primers (200 nM), SYBR™ Green PCR Master Mix (ThermoFisher Scientific) or TaqMan mix (Roche) and Universal Probe Library probes (100 µM) (ThermoFisher Scientific) for the gene of interest. Reactions were performed in triplicate. qPCR analyses were carried out with the FX96 Thermocycler (Biorad, Hercules, USA). Relative mRNA levels were calculated using the Comparative Ct (ΔΔCT) method. Gene expression was normalized with hACTB or mRplp. Primer sequences used are listed in Supplementary Table 1.
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5

Quantitative PCR Analysis of Gene Expression

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RNA was extracted with phenol-chloroform using Upzol (Dutscher, Brumath, France). Synthesis of cDNA was performed using Maxima First cDNA Synthesis Kit (ThermoFisher Scientific) from 1 μg of total RNA. Generated cDNA (50 ng/µL) was used as a template for quantitative PCR (qPCR) run, and mixed with primers (200 nM), SYBR™ Green PCR Master Mix (ThermoFisher Scientific) or TaqMan mix (Roche) and Universal Probe Library probes (100 µM) (ThermoFisher Scientific) for the gene of interest. Reactions were performed in triplicate. qPCR analyses were carried out with the FX96 Thermocycler (Biorad, Hercules, USA). Relative mRNA levels were calculated using the Comparative Ct (ΔΔCT) method. mRNA levels of 2 (Gapdh/Actb) housekeeping genes were used for normalization. Primers sequences and housekeeping genes used are listed in Supplementary Table 1.
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