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5 protocols using platinum sybr green qpcr mix

1

Gene Expression Analysis of Immune Markers

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PP total RNA was purified using the RNeasy Mini Kit (Qiagen) and cDNA was synthesized using the M-MLV Reverse Transcriptase (Promega). Real-time (RT) PCR was performed in the CFX96 Real Time System (Bio-Rad) according to the manufacturer’s instructions, using the Platinum SYBR Green qPCR Mix (Thermo Fisher) and with the following primers: Gp2-F 5′-CTGCTACCTCGAAGGGGACT-3′; Gp2-R 5′-CATTGCCAGAGGGAAGAACT-3′; Spib-F GCCCACACTTAAGCTGTTTGTA-3′; Spib-R 5′-CTGTCCAGCCCCATGTAGAG-3′; Ccl20-F 5′-GATGGCCGATGAAGCTTGTG-3′; Ccl20-R 5′-GACTCTTAGGCTGAGGAGGTTC-3′; Rankl-F 5′-AAACAAGCCTTTCAGGGGGC-3′; Rankl-R 5′-TCCAACCATGAGCCTTCCATC-3′; Ccl19-F 5′-CCTTAGTGTGGTGAACACAACA-3′, Ccl19-R 5′-GGGTGCTAATGATGCGGAA-3′, Ccl21-F 5′-GCTGCAAGAGAACTGAACAGACA-3′, Ccl21-R 5′-CGTGAACCACCCAGCTTG-3′, Cxcl13-F 5′-TCTCTCCAGGCCACGGTATTCT-3′ and Cxcl13-R 5′-ACCATTTGGCACGAGGATTCAC-3′, b2m-F 5′-TTCTGGTGCTTGTCTCACTGA-3′, b2m-R 5′-CAGTATGTTCGGCTTCCCATTC-3′. Data were normalized to the housekeeping gene (b2m), analyzed using the 2ΔΔCT method, and expressed relative to control groups as indicated.
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2

Gene Expression Analysis of Immune Markers

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PP total RNA was purified using the RNeasy Mini Kit (Qiagen) and cDNA was synthesized using the M-MLV Reverse Transcriptase (Promega). Real-time (RT) PCR was performed in the CFX96 Real Time System (Bio-Rad) according to the manufacturer’s instructions, using the Platinum SYBR Green qPCR Mix (Thermo Fisher) and with the following primers: Gp2-F 5′-CTGCTACCTCGAAGGGGACT-3′; Gp2-R 5′-CATTGCCAGAGGGAAGAACT-3′; Spib-F GCCCACACTTAAGCTGTTTGTA-3′; Spib-R 5′-CTGTCCAGCCCCATGTAGAG-3′; Ccl20-F 5′-GATGGCCGATGAAGCTTGTG-3′; Ccl20-R 5′-GACTCTTAGGCTGAGGAGGTTC-3′; Rankl-F 5′-AAACAAGCCTTTCAGGGGGC-3′; Rankl-R 5′-TCCAACCATGAGCCTTCCATC-3′; Ccl19-F 5′-CCTTAGTGTGGTGAACACAACA-3′, Ccl19-R 5′-GGGTGCTAATGATGCGGAA-3′, Ccl21-F 5′-GCTGCAAGAGAACTGAACAGACA-3′, Ccl21-R 5′-CGTGAACCACCCAGCTTG-3′, Cxcl13-F 5′-TCTCTCCAGGCCACGGTATTCT-3′ and Cxcl13-R 5′-ACCATTTGGCACGAGGATTCAC-3′, b2m-F 5′-TTCTGGTGCTTGTCTCACTGA-3′, b2m-R 5′-CAGTATGTTCGGCTTCCCATTC-3′. Data were normalized to the housekeeping gene (b2m), analyzed using the 2ΔΔCT method, and expressed relative to control groups as indicated.
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3

Quantitative RT-qPCR Gene Expression Analysis

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mRNA was extracted using RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. 1.5–2 μg of RNA was used for reverse transcription using Super-Script III First-Strand Synthesis kit (Invitrogen) with random hexamers. Platinum SYBR Green qPCR mix (Invitrogen) was used for amplification on a 7900HT Fast Real Time PCR machine (Applied Biosystems). Expression values were normalized against β-actin. Three independent repeats of each RT-qPCR time course were performed and three independent samples at each time point of each repeat were analyzed. For a complete list of used primers, see S3 Table. qPCR data presented in Fig 1, S1 Fig, and S6 Fig show one representative repeat and show mean ± standard deviation. The heat map in S2B Fig was plotted using Graphpad Prism 7.
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4

Transcriptome Analysis of Gene Expression

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RNA was extracted using the RNeasy Plus Mini Kit from Qiagen. We determined the quality and quantity of RNA using the RNA 6000 Nano kit on the Bioanalyzer instrument (Agilent). We converted RNA into cDNA with the High Capacity cDNA Reverse Transcription Kit (ABI) and performed quantitative PCR using the Platinum SYBR Green qPCR Mix (Invitrogen). Relative gene expression levels were measured using the ΔΔCt method and we evaluated statistical significance with t-test as implemented in the R software (v. 3.0.0). Primer sequences are listed in Additional file 1: Table S1. Total RNA for RNA sequencing was extracted using the miRNEASY kit (Qiagen). Paired-end RNA sequencing was performed on the Illumina Hiseq 2000 platform. Reads were mapped to the genome using Tophat2 (v.2.0.9) and transcript abundances were estimated using Cufflinks (v.2.2.1).
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5

Developmental Expression of Neuropeptides in Zebrafish

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Total RNA was extracted from at least 15 zebrafish embryos per sample at various stages of development using Trizol Reagent (Invitrogen, Waltham, USA). RNA concentration was measured using Nanodrop 2000c (Thermo Scientific, Waltham, USA). cDNA was produced from 1 μg of RNA using SuperScriptR III reverse transcriptase (Life Technologies, Carlsbad, USA), oligo (dT) primers, random hexamer primers and dNTP mix (Invitrogen). Pixel intensities of reverse transcription PCR (RT-PCR) bands were measured using ImageJ software. Quantitative real-time PCR (qPCR) was performed with Platinum SYBR Green qPCR mix (Invitrogen). Sequences of forward and reverse primers were: nphs1 (Fw) 5’-GCAAGCTACATGTATGTAGACGTGT-3’ and nphs1 (Rv) 5’-TCCTGTGAAATGCTGCTGGTGTC-3’,adcyap1a (Fw) 5’-CGCCTCTGAGTTACCCGAAAA-3’ and adcyap1a (Rv) 5’-TAGCGAGCCGCCGTCCTTTG-3’,adcyap1b (Fw) 5’-TCAGGGAAGAGGTGCTGTGAGGA-3’ and adcyap1b (Rv) 5’-CATCTGTTTTCGGTAGCGACTGT-3’,vip (Fw) 5’-GGCTCTTCACAAGCGGATAC-3’ and vip (Rv) 5’-ATCATCACTGACCCGCTTTC-3’. As a reference gene, we used Eukaryotic translation elongation factor 1 alpha 1, like 1 (eef1a1l1) (Fw) 5’-CTTCTCAGGCTGACTGTGC-3’ and eef1a1l1 (Rv) 5’-CCGCTAGCATTACCCTCC-3’ [25 (link)].
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