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8 protocols using cdnas

1

NSCLC Patients' RNA Isolation and Quantification

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RNAs were isolated from blood samples of NSCLC patients using the commercial RNA isolation kit (TIANGEN Biotech, Beijing, China) and reversely transcribed to cDNAs (Applied Biosystems, Foster City, CA, USA). Amplification conditions were as follows: 95°C at 5 min and 35 cycles at 95°C for 10 s, 60°C for 30 s, and 72°C for 30 s. Primer sequences were as follows: AK021443, F: 5′-CTTGAACCCAGAAGACAGG-3′, R: 5′-ATGGAACATTAGAGGTAGCAC-3′; GAPDH, F: 5′-CGGATTTGGTCGTATTGGG-3′, R: 5′-GATTTTGGAGGGATCTCGC-3′.
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2

Quantification of miR-328-3p Expression

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Total RNAs were extracted using Trizol reagents (Thermo, USA) according to the manufacturer’s protocol. The quantity and quality of total RNA samples were determined by a NanoDrop machine (DE, USA). Then, 0.5 μg of RNA extracted from clinical tissues or cells was subjected to reverse transcription and cDNAs were obtained (Applied Biosystems, USA) according to the manufacturer’s instructions. To detect the expression of miR-328-3p in the OS tissues and OS cell lines, qRT-PCR analysis was conducted using SYBR Green qPCR Master Mix (Roche, Switzerland). The reaction was conducted by using 1 μL cDNA, 10 μL SYBR Green qPCR Master Mix, 2 μL primers and 7 μL ddH2O, with a total volume of 20 μL. The conditions were as follows: 95 °C for 30 s, followed by 40 cycles of amplification at 95 °C for 5 s, at 59 °C for 30 s and at 72 °C for 30 s. The primer sequences used in our study were as follows: miR-328-3p forward, 5′-CGGGCCTGGCCCTCTCTGCC-3′ and reverse, 5′-CAGCCACAAAAGAGCACAAT-3′; U6 forward, 5′-CTCGCTTCGGCAGCACA-3′ and reverse, 5′-AACGCTTCACGAATTTGCGT-3′. The expression of miR-328-3p was normalized to that of U6 small nuclear RNA. The expression of miR-328-3p was quantified using the 2−ΔΔCT method. ΔCT = CT (miR-328-3p)-CT (U6). CT was threshold cycle number.
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3

Gene Expression Profiling in SLE

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Total mRNAs were extracted from peripheral blood mononuclear cells of SLE patients and controls using the All Prep DNA/RNA mini kit (QIAGEN) and then were reverse-transcribed into cDNAs (Thermo Fisher Scientific). Transcript levels of NCF1, GTF2I, GTF2IRD1 and GAPDH were measured by quantitative real-time PCR using TaqMan assays (Hs00165362_m1, Hs01073660_m1, Hs00249456_m1 and Hs03929097_g1, Thermo Fisher Scientific, respectively). The relative expression levels of NCF1, GTF2I and GTF2IRD1, normalized to those of the housekeeping gene GAPDH, were calculated by the comparative Ct methodl.
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4

DNAM-1 and CD155 Expression Vectors

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cDNAs encoding mouse DNAM-1 and CD155 were obtained from Thermo Fisher Scientific. Mutants of DNAM-1 (Y319F; S326A; N321Q; Y322F) were generated by PCR using the Site-Directed Mutagenesis Kit (QuickChange; Agilent Technologies), according to the instructions of the manufacturer. The resulting cDNAs were verified by sequencing (unpublished data). For expression in YT-S cells, cDNAs coding for DNAM-1 were cloned into the vector pSRα-Puro, which contains the puromycin resistance gene (puro). For expression in Cos-1 cells, cDNAs encoding DNAM-1 or various PTKs were cloned in the vector pXM139. For expression of CD155 in RMA-S cells, the cDNA encoding CD155 was cloned into the retroviral vector pFB-GFP. Grb2-specific siRNAs (SI00300328, SI02654750) and control scrambled siRNAs (1027280) were obtained from QIAGEN. Transfection of siRNAs into YT-S cells was performed as described elsewhere (Guo et al., 2015 (link)).
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5

Amplification and Sequencing of AHAS Gene

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AHAS was identified from the foxtail millet genomes through BLAST searches (E-value cutoff 1 × 10−5). The amino acid sequences were aligned with clustalx software [56 (link)]. The primers AHAS-F (ATGGCCACGACGACCGCCGC) and AHAS-R (TCAATACACGGTCCTGCCAT) were designed to amplificated the whole coding sequences of AHAS, and the amplification products were 1932 length. Primers were synthesized by BGI Biological Technology Co., Ltd. The 50 μl reaction system included 10 μl 5 × GC Buffer, 4 μl 10 mmol dNTP, 0.5 μl 20 pmol primers, and 0.5 μl (100 ng) cDNAs (Thermo Fisher Science, Beijing, China) were supplemented with ddH2O. Using high-fidelity Phushion DNA polymerase (Thermo-Fisher Scientific) in the GeneAmp PCR System 9700 (Thermo-Fisher Scientific). The experimental conditions were as follows: one cycle at 98 °C for 2 min, 35 cycles at 98 °C for 10 s, 65 °C for 30 s and 72 °C for 2 min, followed by a cycle at 72 °C for 7 min.The PCR products were extracted from 1.0% agarose gels and cloned into the pGEM-T Easy Vector plasmid. The recombinant plasmid was then transformed into Escherichia coli DH5α cells and positive clones were sent to Shanghai Shenggong Biological Co., Ltd. for sequencing.
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6

Transcriptomic analysis of stem cells

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Total RNA was isolated from SCs using Trizol reagent (Life Technologies) following the manufacturer’s procedure. RNA concentration and purity were assessed using the Nanodrop ND-2000 spectrophotometer (Thermo Scientific). A total of 500-1000 ng RNA was reverse transcribed according to the High-Capacity cDNA Reverse Transcription Kit to obtain complementary DNAs (cDNAs) (Thermo Scientific). RT-qPCR was performed with SYBR green master mix (TSINGKE) on the LightCycler@96 Real-Time PCR system (Roche) according to manufactures’ instructions. The specific primers are listed in Supplementary Table 3.
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7

Tau Protein Isoforms and Mutations

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The cDNA for wildtype tau (human isoform 0N4R) was purchased from Thermo Scientific, and cDNAs containing mutations V287E, K311A, V318E (tau-MBD) and C291A and C322A (tau-C291/322A) were synthesised by GenScript. The original phGluc plasmids were donated by Prof. Stephen Michnick (University of Montreal). The hGluc fragments were cloned to the C-terminus of tau, tau-MBD and tau-C291/322A in a pcDNA3.1/zeo backbone. All plasmids were sequenced to confirm their identity.
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8

Cardiac Gene Expression Analysis

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RNAs were extracted from rat myocardial tissues using TRIzol (Invitrogen, Carlsbad, CA, USA) and reversely transcribed into complementary deoxyribose nucleic acids (cDNAs) (Thermo Scientific, Waltham, MA, USA). QRT-PCR was conducted by the SYBR Green method with β-actin as the internal reference. Primer sequences were as follows: HMGB1: 5′-TATGGCAAAAGCGGACAAGG-3′ (F) and 5′-CTTCGCAACATCACCAATGGA-3′ (R); KLF2: 5′-GAGCCTATCTTGCCGTCCTT-3′ (F) and 5′-AGCACGCTGTTTAGGTCCTC-3′ (R); eNOS: 5′-CAACTGGAAAAAGGCAGCCC-3′ (F) and 5′-AAGAGCCTCTAGCTCCTGCT-3′ (R); TM: 5′-CCTTTGTCTTTCCGGGCTCT-3′ (F) and 5′-TCAAGTCCTCCCTACCCTCG-3′ (R); and β-actin: 5′-TGCTATGTTGCCCTAGACTTCG-3′ (F) and 5′-GTTGGCATAGGTCTTTACGG-3′ (R).
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