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Quantstudio 5 design and analysis software v1

Manufactured by Thermo Fisher Scientific
Sourced in United States

The QuantStudio™ 5 Design and Analysis Software v1.5.1 is a software application designed to operate the QuantStudio™ 5 Real-Time PCR System. The software provides capabilities for experimental setup, data acquisition, and analysis of real-time PCR experiments.

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4 protocols using quantstudio 5 design and analysis software v1

1

Fatty Liver Gene Expression Analysis

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RNA was extracted from cells treated with FFA, HGF, FFA + HGF and controls using the RNAeasy kit (Qiagen, Germany) as per manufacturer’s instructions. RNA was quantified spectrophotometrically, and all samples were normalized to the lowest concentration in the group. cDNA synthesis was performed using the RT2 First Strand Kit (Qiagen, Germany). The PCR reaction was setup on the RT2 Profiler™ PCR Array Human Fatty Liver, PAHS-157Z (Qiagen, Germany). PCR was performed and analyzed using the QuantStudio™ 5 Design and Analysis Software v1.5.1 (Applied Biosystems, USA). A melt curve analysis was performed to verify PCR specificity.
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2

Genotyping of Hepatocyte DNA

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DNA was isolated from cryopreserved hepatocyte lots using the QIAamp DNA mini kit (Qiagen, Germany). Genotyping was performed using TaqMan SNP Genotyping Assays and TaqPath™ ProAmp™ Master Mix (Thermo Fisher Scientific, USA) as per manufacturer’s recommendations for polymorphisms in PNPLA3, MBOAT7, HSD17β13, and TM6SF2 (Table S2). PCR was performed and analyzed using the QuantStudio™ 5 Design and Analysis Software v1.5.1 (Applied Biosystems, USA).
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3

Quantitative PCR Analysis of Gene Expression

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The total RNA from cells was isolated with Ultraspec or TRIsure (BIO-38032, Bioline USA, Inc., Memphis, TN, USA) and this RNA (1 μg) was then reverse-transcribed using Improm-II reverse transcriptase (Promega, Madison, WI, USA). Polymerase chain reaction (PCR) amplifications were performed using the Power SYBR Green PCR Master Mix kit (Applied Biosystems, Foster City, CA, USA) in a QuantStudio5 (Applied Biosystems, Foster City, CA, USA) with the primer sets indicated below. The data were analyzed with QuantStudio5 Design and Analysis Software v1.4 (Applied Biosystems, Foster City, CA, USA). The following set of primers were used: Epo (forward 5’ -CAAAGTAACTTCTATGCTTGGAAAA-3′ reverse, 5′-CAGGCCTTGCCAAACTTCTATG-3′); Slc7a5 (forward 5′-TTCGCCACCTACTTGCTCAA-3′, reverse 5′-CCTTTACGCTGTAGCAGTTC-3′); 28S (forward 5′-GGTAGCCAAATGCCTCGTCAT-3′, reverse 5′-GGATAGTAGGTAGGGACAGTGGGAAT-3′). For amplification of murine genomic region lacking Slc7a5 exon1 in ErGFPcre Slc7a5LoxP/LoxP mice the following primers were used forward 5′- GGCTCCTGGACTTATCTTGACCAATG-3′ reverse, 5′- GTGGTGCTTTGCTGAAGGCAGGG-3′).19 (link)
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4

RNA Extraction and Quantitative PCR Protocol

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Total RNA from the cells was isolated using Ultraspec or TRIsure (BIO-38032, Bioline USA, Inc., Cincinnati, OH, USA). This RNA (1 µg) was then reverse-transcribed using Improm-II reverse transcriptase (Promega, Madison, WI, USA) and polymerase chain reaction (PCR) amplifications were performed using the Power SYBR Green PCR Master Mix kit (Applied Biosystems, Foster City, CA, USA) in a QuantStudio5 (Applied Biosystems, Foster City, CA, USA). Primer sets used are included in Supplementary Table S1. The data were analyzed with QuantStudio5 Design and Analysis Software v1.4 (Applied Biosystems, Foster City, CA, USA).
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