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5 protocols using mircute plant mirna isolation kit

1

Cotton Total RNA Extraction and cDNA Synthesis

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Total RNA was extracted from cotton using the miRcute Plant miRNA Isolation Kit (Beijing Tiangen Biotech, Beijing, China). RNA integrity was assessed by 1.2% agarose gel electrophoresis with 1 × TAE electrophoresis buffer at 130 V for 20 min. RNA with a 28S:18S ratio of 2:1 was used for subsequent experiments. The concentration of total RNA was measured by a Nanodrop ND1000 spectrophotometer (NanoDrop Technologies, Wilmington, NC, USA).
The cDNA of the target genes was synthesized using the Easyscript® One-Step gDNA Removal and cDNA Synthesis SuperMix Kit (Beijing TransGen Biotech, Beijing, China). In a 20 µL reaction system, 1 µg total RNA, 10 µL 2 × ES reaction mixture, 1 µL Oligo(dT)18 primer, 1 µL Easyscript® RT/RI Enzy Mix, 1 µL gDNA remover, and variable RNase-free water were mixed. The mixture was incubated at 42 °C for 30 min, followed by 85 °C for 5 s. For miRNA cDNA synthesis, a miRNA-specific stem-loop RT primer was used. The reaction was incubated at 16 °C for 30 min, followed by 30 °C for 30 s, 42 °C for 30 s, and 50 °C for 20 s for 60 cycles. Finally, the reaction was stopped at 85 °C for 5 s.
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2

Quantitative Analysis of miRNAs and Target Genes in 'Feng Dan' Leaves

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miRNAs of ‘Feng Dan’ leaves were extracted using a miRcute Plant miRNA Isolation Kit (TIANGEN, Sichuan, China), and then cDNAs were synthesized using a miRcute Plus miRNA First-Strand cDNA Synthesis Kit (TIANGEN). A ubiquitin (UBQ) gene was used as reference [29 (link)]. A miRcute Plus miRNA qPCR Detection Kit (SYBR Green) (TIANGEN, including universal reverse primer) was used for qRT-PCR with a tailing method.
RNAs of ‘Feng Dan’ leaves were extracted using a RNAprep Pure Plant Plus Kit (Polysaccharides & Polyphenolics-rich) (TIANGEN), and then cDNAs were synthesized using a PrimeScript™ RT reagent Kit with gDNA Eraser (Perfect Real Time) (TakaRa, Shiga, Japan). A Tubulin-β gene was used as reference [30 ]. A TB Green® Premix Ex Taq™ II (Tli RNaseH Plus) (TakaRa) kit was used for qRT-PCR.
Three replicates were included for each sample respectively. Primers used for qRT-PCR are listed in Appendix Table 1. The expression levels of ptc-miR396g-5p and its target gene were calculated using the formula of 2−ΔΔCt [31 (link)]. Statistical analysis was performed using Excel and SPSS 21.0.

Primers for qRT-PCR.

Table 1
PrimersSequences (5′-3′)
ptc-miR396g-5p (Forward)CGGTTCCACGGCTTTCTTGACT
UBQ (Forward)TACCCAAACAGCCCTCCAAC
psu.T.00022975 (Forward)GGCACCAAGGTCAGCAACTA
psu.T.00022975 (Reverse)TGGAATGACGCATAGGAGGA
Tubulin-β (Forward)TTGAGAACGCCGACGAGTGT
Tubulin-β (Reverse)ACCAGGAAAACGAAGGCAGC
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3

Isolation and Reverse Transcription of Plant miRNAs

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miRNAs were isolated from the petals of 42 tree peony varieties using the miRcute Plant miRNA Isolation Kit (Tiangen, Beijing, China). Then, miRcute Plus miRNA First-Strand cDNA Synthesis Kit (Tiangen, China) was used to synthesize the first strand. Reaction system (20 μL): Total miRNA 2 μL, 2× miRNA RT Reaction Buffer 10 μL, miRNA RT Enzyme Mix 2 μL, and RNase-free ddH2O 6 μL. The reaction procedure was as follows: 42 °C for 60 min and 95 °C for 3 min.
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4

miRNA Extraction and Synthesis Protocol

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Total miRNA was extracted using a miRcute Plant miRNA Isolation Kit (TIANGEN). miRNA quality and purity were checked using the same method as for total RNA. miRNA cDNA, which was later used as a template for expression studies, was synthesized using a miRcute Plus miRNA First-Strand cDNA Kit (TIANGEN). The reaction system comprised 4 μL total miRNA, 10 μL 2× miRNA RT Reaction Buffer, 2 μL miRNA RT Enzyme Mix, and ddH2O to adjust the volume to 20 μL. A reverse transcription program of 42°C for 15 min and 95°C for 3 min was utilized.
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5

Quantifying Plant and Fungal miRNA Expression

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We extracted total RNA using the miRcute Plant miRNA Isolation Kit (Tiangen, Beijing, China). Expression of miRNA was detected by stem–loop qRT-PCR as described [62 (link)]. First-strand cDNA was synthesised by miRNA First Strand cDNA Synthesis (Vazyme, Nanjing, China) with the stem-loop RT primer. The small nuclear RNA U6 (in fungi) and 5.8 rRNA (in plant) was used as control. Transcript levels of genes were analysed by qRT-PCR, which was performed using RealStar Green Power Mixture (GenStar, Beijing, China). MdEF1α of M. domestica and G6PDH of V. mali were used as the reference genes, respectively. Relative expression of genes was calculated using the 2-ΔΔCt method [63 (link)]. All primers used in this study are listed in Table S5 (see online supplementary material).
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