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22 protocols using blend taq

1

PCR Amplification and Gel Electrophoresis

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PCR amplification was performed in 10 μL reaction volumes consisting of 0.1 μL of Blend Taq® (Toyobo, Osaka, Japan) (2.5 units/μL), 1.0 μL of 10 × buffer for Blend Taq®, 1.0 μL dNTP (2 mM each), 0.2 μL each of forward and reverse primers (10 μM), and 1.0 μL of template DNA (40 ng/μL), under the following conditions: denaturation for 5 min at 95°C; 30 cycles of denaturation at 95°C for 30 s, primer annealing at 55°C for 30 s, and primer extension at 72°C for 30 s.
The resulting PCR products were analyzed using electrophoresis on 4% or 2% agarose gels and visualized by staining with ethidium bromide. Agarose suitable for low molecular weight DNA fragment separation (Agarose KANTO HC; Kanto Chemical, Tokyo, Japan) was used for 4% gels, whereas standard agarose (Agarose-LE; Nacalai Tesque, Tokyo, Japan) was used for 2% gels.
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2

TGF-β Transcriptional Response Assay

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The LLC cells were seeded at 3 × 105 cells/dish in 6 cm dishes 1 day before the experiments. The cells were starved overnight with DMEM containing 0.3% FCS and stimulated with or without 5 ng/mL TGF‐β for the indicated times. Total RNA was isolated using the ReliaPrep RNA Cell Miniprep System (Promega, Madison, WI, USA). Reverse transcription was carried out with the PrimScript II First Strand, Osaka, Japan cDNA Synthesis Kit (Takara, Ohtsu, Japan). RT‐PCR was performed with BlendTaq (TOYOBO). β‐actin was used as an internal control. The primer sequences used are described in Table 1.
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3

VLDLR mRNA Splicing Variant Analysis

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The two types of Vldlr mRNA splicing variants, type 1 and type 2, generated by alternative splicing of exon 16, were analyzed by RT-PCR with Blend Taq (Toyobo) and primers sandwiching exon 16 according to the method of Sakai et al. (primer sequences are shown in Table 219 (link)). Total RNA extraction from the liver and cDNA synthesis were performed as described above. It was confirmed that the amplification did not reach a plateau under the 30-cycle condition used for measurement. Figure 2E contains a cropped image, and Fig. S5 shows a full-size unmodified image.
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4

DNA Amplification and Ligation Reagents

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Blend Taq® and Taq DNA polymerase were purchased from TOYOBO (Osaka, Japan) and New England Biolabs (Ipswich, MA, USA), respectively. T4 DNA Ligase was purchased from Takara Bio (Kusatsu, Japan). Restriction enzymes were purchased from Takara Bio and TOYOBO. Other general reagents were purchased from Wako Pure Chemical Industries (Osaka, Japan) and Nacalai Tesque (Kyoto, Japan).
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5

Quantitative Expression Analysis of Genes

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PCR was performed using Blend Taq (Toyobo, Tokyo, Japan) and a GeneAmp PCR System 9700 thermal cycler (Applied Biosystems,
Branchburg, NJ, USA). The primers used in the present study were designed, and summarized in Table 1 Primer sequence used for RT-PCR and Real-time PCR
GeneSequence (5′–3′)Length (bp)
RT-PCR
Krt19
ForwardGTGTCTGATGGGCTGCTGTCT539
ReverseCTCAGGATCTTGGCTAGGTCG
Vim
ForwardGGCCGAGGAATGGTACAAGTC320
ReverseGGGCCATCTTAACATTGAGCAG
ERa
ForwardCTAATTCTGACAATCGACGC347
ReverseGTGCTTCAACATTCTCCCTCCTC
ERb
ForwardGGTGTCTGGTCCTGTGAAGGATGT670
ReverseCCGTCGTCGCCAGGAGCATGTCAA
RpL19
ForwardGAAATCGCCAATGCCAACTC406
ReverseTGAGGCTCGCAGGTCTAAGA

Real-time PCR
class1 Igf1
ForwardGCAGCCTTCCAACTCAATTATTTAA89
ReverseGTAGAAGAGGTGTGAAGACGACATG
class2 Igf1
ForwardCACCTGTTCTTAAGTCCTCAGTTTTG143
ReverseGTAGAAGAGGTGTGAAGACGACATG
RpL19
ForwardCCGCAGCCATGAGTATGCT60
ReverseCGCAGCGGAGGACACTAGA
. The PCR conditions were as follows: 2 min at 94 C; an appropriate number of cycles of 94 C for 30 sec, 60 C
for 30 sec and 72 C for 30 sec; and a final step at 72 C for 10 min. Aliquots (9 µl) of each reaction were electrophoresed on
2% agarose gels, stained with ethidium bromide and photographed under ultraviolet light.
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6

Adipose-Derived Stem Cell Culture

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Culture reagents were from Gibco (Grand Island, NY, USA). ADSCs were cultured in a conventional medium that consisted of Dulbecco’s Modified Eagle’s Medium (DMEM), supplemented with 100-U/mL penicillin G sodium, 100-mg/mL streptomycin sulfate, and 10% vol/vol FBS. Unless otherwise stated, all the other reagents were from Sigma (St. Louis, MO, USA). VPA was from Suju (Guangzhou, China). RG108, Reprogramming Cocktail Set I and purmorphamine were from Biovision (San Francisco, USA). Cell Counting Kit-8 (CCK-8) was from Dojindo (Kyushu, Japan). Cell Cycle and Apoptosis Analysis Kit and Annexin V-FITC/PI apoptosis detection kit were from KeyGEN (Nanjing, China). Monoclonal anti-vimentin (NeoMarkers) was from Lab Vision Corp (Fremont, MO, USA). Goat anti-CD34 polyclonal antibody, goat anti-mouse IgG and goat anti-rabbit IgG were from Santa Cruz Biotechnology (Santa Cruz, CA, USA). EZgeneTM Tissue RNA Miniprep Kit was from Biomiga (San Diego, CA, USA). ReverTra Ace qPCR RT Kit, Blend Taq and Blend Taq-Plus were from Toyobo (Osaka, Japan). Primers were synthetized by BGI (Shenzhen, China).
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7

Transcriptional Analysis of ER Stress Response

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Cells grown to exponential phase were incubated with YPD medium containing 2 μg/ml tunicamycin or 4 mM DTT, and harvested at the indicated times. Total RNA was then prepared using ISOGEN reagent (Nippon Gene) and the RNeasy Mini kit (Qiagen). First strands of cDNA were generated using the PrimeScript RT reagent Kit (Takara). The HAC1 cDNA was amplified from first strands of cDNA with Blend Taq (TOYOBO), and then analyzed by agarose gel electrophoresis. Detection, quantification, and statistical analysis was carried out by using a LAS-4000 (Fuji Film), ImageQuant (GE Healthcare), and Excel (Microsoft), respectively. The cDNAs of ERO1, KAR2, and SSK1, were quantitated by a quantitative real-time RT-PCR (qRT-PCR) method using a 7500 fast real-time RT-PCR system (Applied Biosystems) with SYBR Premix Ex Taq (Takara). A standard curve was generated from diluted RNA derived from wild-type cells, and levels of gene expression were normalized to ACT1 expression. HAC1 primers (CTGGCTGACCACGAAGACGC and TTGTCTTCATGAAGTGATGA) were used to monitor splicing of HAC1 mRNA. ERO1 primers (TAACAGCAAATCCGGAACG and ACCAAATTTGACCAGCTTGC), KAR2 primers (AGACTAAGCGCTGGCAAGCT and ACCACGAAAAGGGCGTACAG), SSK1 primers (AGCTGGAAGCAGGGAGAAAG and TGAGTGAGGGTTGGAAGGTG), and ACT1 primers (TGCCGAAAGAATGCAAAAGG and TCTGGAGGAGCAATGATCTTGA) were used to analyze the mRNA level of ERO1, KAR2, and SSK1.
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8

Islet RNA Extraction and qPCR Analysis

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Tissues were obtained from female C57/BL6 mice and immediately homogenized in guanidine isothiocyanate solution. Islets were isolated as previously described [9 (link)]. Total RNA extraction and cDNA synthesis were performed as described above. PCR reactions were carried out with Blend Taq (Toyobo) using the following cycling conditions: 94°C for 2 min followed by 25–30 cycles of 94°C for 30 s, 60°C for 30 s, and 72°C for 60 s. Rpl32 expression was used as an internal control [10 (link),11 (link)]. The sequences of the primers used are shown in Table 1.
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9

Cloning and Expressing laEBLN-1 Isoforms

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cDNAs reverse-transcribed from laEBLN-1v1 and laEBLN-1v2 mRNAs were amplified by PCR using Blend taq (TOYOBO) with the primer pairs listed in S5 Table. The PCR product of laEBLN-1v1 was ligated into 3×FLAG-CMV-14 vector (SIGMA) using Ligation high ver.2 (TOYOBO) after digestion with the restriction enzymes HindIII and BamHI (New England Biolabs) at 37°C for 60 min. The PCR product of laEBLN-1v2 was ligated into V5-His-TOPO vector (Life Technologies) according to manufacture’s instructions. The plasmids transformed into TOP10 Competent Cells (Life Technologies) were collected using PureYield Plasmid Midiprep System (Promega) after confirming the insert with nucleotide sequencing. In addition, sub-cloning of ORFs in laEBLN-1v1 and laEBLN-1v2 into pcDNA3.10 vector (Thermo Fisher Scientific) was conducted using the above plasmids as templates for PCR, which were digested with HindIII and BamHI (New England Biolabs).
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10

Preimplantation Embryo RNA Extraction and RT-PCR

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Total RNAs of preimplantation embryos were extracted with Trizol reagent (Invitrogen) and cDNAs synthesized using SuperScript III reverse transcriptase (Invitrogen), according to the manufacturer’s protocol. PCR was performed with Blend Taq (Toyobo) for 40 cycles of 94 °C for 30 sec, 60 °C for 30 sec, and 72 °C for 30 sec. Primers used are shown in Supplementary Table.
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