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17 protocols using dna polymerase

1

Molecular Detection of BHV-1 Genes

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DNA was extracted from nasal swabs and the supernatant of the infected cells using the Ezup column viral DNA kit (Sangon Biotech, China). Specific primers were designed to amplify BHV-1 US7, US8, UL48, and UL49 genes (Supplementary Table S1). PCR reactions were amplified using DNA polymerase (Vazyme Biotech, China) under the conditions: 95°C for 3 min, 35 cycles at 95°C for 15 s, 68°C for 1 min, and 72°C for 2 min (Waters and Shapter, 2014 (link)).
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2

Genotyping Mouse DNA by PCR

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Each mouse genotype was identified by PCR amplification and electrophoresis.27 DNA was extracted according to the manufacturer's instructions (TransGen, China). DNA polymerase (Vazyme, China) and two primer pairs (Table 1) were used for PCR amplification under the following amplification conditions: 95 °C for 3 min; 35 cycles of 95 °C for 15 s, 60 °C for 15 s and 72 °C for 2.5 min; and 72 °C for 5 min. PCR products were visualized by 1.5% agarose gel electrophoresis (Invitrogen, USA).
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3

Transcriptional Analysis of Bcl-2 and Nur77 in Cell Lines

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Total RNAs of MEF-WT, Bcl2−/−MEF, Hela-WT and Nur77−/−HeLa cells were prepared using Trizol Reagent (Takara Biomedical Technology) according to the Manufacturer's Instructions. The cDNAs were obtained by using a Reverse Transcription Kit (Yeasen Biotechnology). Primers used for PCR amplification using DNA Polymerase (Vazyme Biotech) were based on the DNA sequences of Bcl-2 and Nur77 from the PubMed Database:
Nur77 (F: 5′- ATGCCCTGTATCCAAGCCCAA-3′, S: 5′-TCAGAAGGGCAGCGTGTCCAT-3′);
Bcl-2 (F: 5′-ATGGCGCAAGCCGGGAGAACA-3′, S: 5′- TCACTTGTGGCCCAGGTATGC-3′),
and the amplified products were identified by Agarose Gel Electrophoresis (Biosharp).
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4

Transcriptional Analysis of Bcl-2 and Nur77 in Cell Lines

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Total RNAs of MEF-WT, Bcl2−/−MEF, Hela-WT and Nur77−/−HeLa cells were prepared using Trizol Reagent (Takara Biomedical Technology) according to the Manufacturer's Instructions. The cDNAs were obtained by using a Reverse Transcription Kit (Yeasen Biotechnology). Primers used for PCR amplification using DNA Polymerase (Vazyme Biotech) were based on the DNA sequences of Bcl-2 and Nur77 from the PubMed Database:
Nur77 (F: 5′- ATGCCCTGTATCCAAGCCCAA-3′, S: 5′-TCAGAAGGGCAGCGTGTCCAT-3′);
Bcl-2 (F: 5′-ATGGCGCAAGCCGGGAGAACA-3′, S: 5′- TCACTTGTGGCCCAGGTATGC-3′),
and the amplified products were identified by Agarose Gel Electrophoresis (Biosharp).
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5

Optimizing Recombinant Protein Expression

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pCold I and pCold TF vectors, as well as restriction endonucleases, were purchased from Takara Corporation (Dalian, China). DNA polymerase and T4 DNA ligase were obtained from Vazyme Biotechnology Corporation (Nanjing, China). The ClonFast kit was acquired from Obio Technology Corporation (Shanghai, China). 2,2′-Dipyridyl, DTT, L-cysteine, L-alanine, L-glutathione reduced (GSH), and deamino-NADH were purchased from Merck (Darmstadt, Germany). Pyridoxal-5′-phosphate was obtained from Sangon Biotechnology Corporation (Shanghai, China). All primers were synthesised by BGI (Shenzhen, China). The remaining chemicals were of analytical grade.
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6

Construction of pEGFP-N1 Recombinant Plasmid

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The pEGFP-N1 (cat. no. 6085-1; Addgene, Inc.) plasmid was maintained within our laboratory. Normal Donkey serum (cat. no. D9663) was purchased from Sigma-Aldrich; Merck KGaA. Opti-MEM, DMEM high glucose medium, trypsin and FBS were purchased from Gibco; Thermo Fisher Scientific, Inc., and Lipofectamine® 2000 and TRIzol® were purchased from Invitrogen; Thermo Fisher Scientific, Inc. Anti-α-tubulin and anti-tyrosinated tubulin antibodies were supplied by Sigma-Aldrich; Merck KGaA. The homologous recombination kit (cat. no. C122-02; Vazyme Biotech Co., Ltd.), DNA Polymerase (cat. no. P508-d1; Vazyme Biotech Co., Ltd.) and PrimeScript™ IV 1st strand cDNA synthesis mix (cat. no. 6215A; Takara Biotechnology Co., Ltd.) were used for construction of the recombinant plasmid, and the water used in the present study was ultra-pure (R≥18 M Ω/cm).
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7

Quantitative Gene Expression Analysis

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DNA was amplified by DNA polymerase (Vazyme Biotech Co., Ltd, Nanjing, Jiangsu, China). The qPCR analysis was then performed using the TB Green® Premix Ex Taq™ (Takara Holdings Inc., Kyoto, Japan) on the Real-Time PCR system (Applied Biosystems, Foster City, CA, USA). Relative expression values of gene were calculated by the 2-△△Ct method. GAPDH was used as the endogenous loading.
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8

Genetic Manipulation of Oyster Mushroom

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The dikaryotic P. ostreatus strain CCMSSC00389 from the Center for Mushroom Spawn Standards and Control of China was used in this study as a parent strain for OE and RNAi experiments. The WT, OE and RNAi strains were maintained on potato dextrose agar (PDA) at 4 °C. For the selection and maintenance of transformants, complete media (CM) was supplemented with 90 μg/mL hygromycin (hyg) (Invitrogen, U.S.A.). Agrobacterium tumefaciens (A. tumefaciens) GV3101 (IMCAS, Beijing, China) was grown in Luria-Bertani (LB) medium (Oxoid, England) containing 100 μg/mL kanamycin (kan) (VWR Life Science, U.S.A.) and 50 μg/mL rifampicin (rif) (MP Biomedicals, France) and used to transform P. ostreatus. Escherichia coli (E. coli) DH5α and BL21 (DE3) (Tiangen, Beijing, China) were used for plasmid construction, and grown in LB broth containing kan (50 μg/mL). Restriction endonucleases were purchased from New England Biolabs (NEB), and DNA polymerase, a reverse-transcription kit, and a DNA Gel Extraction kit were purchased from Vazyme (Nanjing, China). Primer synthesis and DNA sequencing were performed by Sangon Biotech (Shanghai, China). The plasmid pCAMIBA 1300 was purchased from YRGen Biotech Company (Changsha, China).
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9

Genotyping Slc30a3 Knockout Mice

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Fresh mouse tail clips were dissolved in tail lysis buffer at 55°C for 12 hours. Genomic DNA was extracted using absolute ethanol and 70% ethanol. Genotyping was performed by polymerase chain reaction using DNA polymerase (Vazyme, Nanjing, China, Cat# P222). To verify the deletion of Slc30a3 in the retina of ACs or RGCs, genomic DNA was extracted and amplified using the primers GPS00001161-Slc30a3-5wt-tF1 and GPS00001161-Slc30a3-5wt-tR1 (primer information is presented in Additional Table 1). The amplicon size for Slc30a3 wild-type (WT) was 202 bp and Slc30a3 was 304 bp (Additional Table 1). The presence of VGAT-Cre was verified using 12785 and oIMR8292 primers (amplicon size 200 bp), and primers 12786 and 12785 were used to identify the WT allele (323 bp) (Additional Table 1). We used C57BL/6J (wt/wt) mice, VGATCreZnT3fl/fl (mut/wt; Slc30a3fl/fl) mice, and blank control (water) for grouping. The presence of VGLUT2-Cre was determined by polymerase chain reaction using primers 13007 and 32667, with amplicon sizes of 124 (mutant) and 245 (WT) bp (Additional Table 1). We used C57BL/6J (wt/wt) mice, VGLUT2CreZnT3fl/fl (mut/wt; Slc30a3fl/fl) mice, and blank control (water) for grouping.
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10

Lipid Quantification by Enzymatic Assay

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PC (95% purity, from soybeans) was purchased from Avanti Polar-Lipids, Inc. (Alabaster, AL, USA). Peroxidase (from horseradish), choline oxidase (from Alcaligenes sp.), and PS standards were purchased from Sigma-Aldrich Co. (St. Louis, MO, USA). DNA polymerase was obtained from Vazyme (Nanjing, China). IPTG and L-arabinose were purchased from Solarbio (Beijing, China). 2-Propanol and n-hexane were purchased from the EMD Millipore Corporation (Billerica, MA, USA). All other chemicals and organic solvents were analytical grade reagents.
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