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26 protocols using pcr primers

1

Reagent Procurement and Primer Design

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All reagents were purchased from Wako (Osaka, Japan) unless otherwise noted. All PCR primers were purchased from Sigma-Aldrich (Tokyo, Japan) or Eurofins Genomics (Tokyo, Japan). The primer
sequences and antibodies used in this study are listed in Supplementary Tables 1 and 2 (online only), respectively.
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2

Reagent Procurement for PCR Analysis

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All reagents were purchased from Wako (Osaka, Japan), unless otherwise stated. All PCR primers were purchased from either Sigma-Aldrich (Tokyo, Japan) or Eurofins Genomics (Tokyo, Japan).
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3

Biochemical Assays and Cytokine Quantification

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RES raw powders were purchased from Sigma Chemical Co. (St. Louis, MO, USA), while ISO injection was obtained from a local pharmacy. L-RES was purchased from Lipolife, UK. L-RES has a particle size less than 200 nm with a neutral zeta potential as stated by the manufacturer. Urea, creatinine and uric acid biochemical assays were supplied from Randox, Crumlin, UK. IL-6 ELISA kit was obtained from R&D Systems (Minneapolis, MN, USA). MAPK, cystatin c and β-actin antibodies were purchased from Novus Biologicals (Centennial, CO, USA). The PCR primers were obtained from Sigma (St. Louis, MO, USA).
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4

Gastrocnemius and Liver RNA Extraction

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Total RNA was extracted from the mouse gastrocnemius muscles and the liver using isogen (Wako Pure Chemical Industries Ltd.), according to the manufacturer's instructions. Reverse transcription (RT) polymerase chain reaction (PCR) was performed using total RNA samples obtained from the gastrocnemius and the liver using an ABI 7300 system (Applied Biosystems). Real‐time PCR using the DNA‐binding dye SYBR Green was used for detection of the PCR products for RNA sample obtained from cells after synthesized cDNA. The following PCR primers (Sigma‐Aldrich Japan K.K., Hokkaido, Japan) were used: FGF21, 5′‐CAGGGAGGATGGAACAGTGGTA‐3′ (forward) and 5′‐TGACACCCAGGATTTGAATGAC‐3′(reverse); β‐actin, 5′‐TATCCACCTTCCAGCAGATG‐3′ (forward) and 5′‐AGCTCAGTAACAGTCCGCCTA‐3′ (reverse). The respective ratios of the other signals to that of β‐actin were calculated for all samples. Normalized values were expressed as a relative value using the value of the RUN group as 1.
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5

Antibody Production and Characterization

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Phosphate-buffered saline (PBS), 4-aminobenzoic acid, N-hydroxysuccinimide (NHS), 1-ethyl-3-(3-dimethylaminopropyl)-carbodiimide (EDC), and PCR primers were purchased from Sigma-Aldrich (Germany). Potassium hexacyanoferrate (III), hexaammineruthenium (III), sodium nitrite, hydrochloric acid, and dipotassium phosphate monopotassium phosphate were purchased from ChemPur (Poland). An ExtractMe DNA Bacteria kit was purchased from Blirt (Poland), and a SensiFAST SYBR No-ROX kit was purchased from Bioline (UK). Phosphate buffer with different pH (5.68, 7.01, 7.99) was prepared by mixing the K2HPO4 and KH2PO4 in different ratios. All reagents were used without further purification. Aqueous solutions were prepared with the usage of double-distilled sterile water (ddH2O).
All biomaterials utilised in this manuscript are accurately described elsewhere [30 (link)]. Herein, we present them briefly. The monoclonal mouse antibodies were produced by the Nanobioengineering Laboratory at the Polish Center for Technology Development Ltd. through procedures described elsewhere [31 ], with slight changes. Recombinant protein D was isolated at the Institute of Biotechnology and Molecular Medicine following the standard procedures. The efficiency and quality of antibody production were verified with the ELISA test (data are not shown).
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6

Reagent and Primer Procurement Protocol

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All reagents were purchased from Wako (Osaka, Japan) unless otherwise noted. All PCR primers were purchased from Sigma-Aldrich (Tokyo, Japan) or Eurofins Genomics (Tokyo, Japan).
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7

Quantitative RT-PCR Analysis of Shh Expression

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Total RNA was harvested by using the Rneasy Kit (Qiagen, Valencia, CA, USA). CDNA synthesis was done with Superscript II (40 U/l, Invitrogen, Groningen, The Netherlands). Real-time PCR was performed using the Biorad-iCycler IQ detector system and Biorad-iCycler IQ SYBR Green mix (Biorad, Munich, Germany). The PCR primers (Sigma Chemical Company, St. Louis, MO, USA) were: Shh 5'-CAGCGACTTCCTCACTTTCC-3' (forward) and 5'-GGAGCGGTTAGGGCTACTCT-3' (reverse); GAPDH: 5'-ACAGTCAGCCGCATCTTCTT-3' (forward) and 5'-ACGACCAAATCCGTTGACTC-3' (reverse). Fluorescent threshold values were measured in triplicate, and fold changes were calculated by the formula 2-(sample 1 ΔCt - sample 2 ΔCt), where ΔCt is the difference between the amplification fluorescence thresholds of the mRNA of interest and the GAPDH mRNA.
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8

Sanger Sequencing Variant Validation

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Dideoxy Sanger sequencing was used to validate candidate variants and to genotype candidate variants in the larger non-HHS control cohort (Table 1). Polymerase chain reaction (PCR) primers (Sigma-Aldrich) were designed using Primer-blast44 (link) targeting 100- to 200-bp region flanking target SNVs, and primer quality was tested using OligoAnalyzer 3.1 (https://www.idtdna.com/calc/analyzer). Details of the primers utilized are given in Table S1 (available as supporting information in the online version of this paper). PCR amplification was done using DNA polymerase (PrimeSTAR GXL, Clontech Laboratories) with patients’ DNA as template, according to manufacturer’s instructions (annealing temperature 638C). PCR products were visualized (1% agarose gel stained with ethidium bromide) and then sequenced (Genewiz).
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9

Quantification of Autophagy-Related Genes

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Reverse transcription‐PCR was performed using total RNA samples obtained from muscle tissues as described previously.26 Real‐time PCR using the DNA‐binding dye SYBR Green was employed for the detection of PCR products for RNA sample obtained from cells after synthesized cDNA. The following PCR primers (Sigma‐Aldrich Japan, Hokkaido, Japan) were used: p62/SQSTM1, 5′‐TGTGGAACATGGAGGGAAGAG (forward) and 5′‐TGTGCCTGTGCTGGAACTTTC (reverse); MAP1lc3b (LC3B), 5′‐GACGGCTTCCTGTACATGGTTT (forward) and 5′‐TGGAGTCTTACACAGCCATTGC (reverse); Beclin‐1, 5′‐GTGCGCTACGCCCAGATC (forward) and 5′‐GATGTGGAAGGTGGCATTGAA (reverse); and GAPDH, 5′‐TGTGTCCGTCGTGGATCTGA (forward) and 5′‐CCTGCTTCACCACCTTCTTGA (reverse). The ratio of the other signals to that of GAPDH was calculated for every sample.
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10

Genotyping AhR Knockout Mice

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Genotyping was performed with two sets of PCR primers (Sigma Aldrich, Gillingham, UK). The first amplified a region of AhR exon 2 present in the wild type but not the knockout mice, that is, forward TTCAGAGTAAAGCCCATCCC and reverse ATCAAAGAAGCTCTTGGCCC. The second set amplified a region of the neomycin gene only present in the knockout animals, that is, forward TGGGTGGAGAGGCTATTC and reverse ATGGTGAGATGACAGGAGATC (http://blast.ncbi.nlm.nih.gov/). Mice were genotyped prior to experimentation using DNA derived from ear clip tissue.
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