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41 protocols using first strand cdna synthesis kit

1

Quantifying Hormone-Induced Gene Expression in Kiwifruit

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Total RNA was extracted from various kiwifruit samples (samples taken before and after each hormone/stress treatment) using the RNA Midi Kit (OMEGA, Guangzhou, China), following the manufacturer’s protocols. RNA extraction was conducted in triplicate using three biological replicates. Subsequently, reverse transcription was carried out using the First-Strand cDNA Synthesis Kit (Vazyme, Nanjing, China). For quantitative real-time PCR (qRT-PCR), the Thermo Scientific Pikoreal Cycler 96 Real-Time PCR system was employed with SYBR Green Master Mix (Vazyme, Nanjing, China). The internal control for mRNA was AeActin1, and the relative expression levels of genes were determined using the 2−∆∆CT method [41 (link)]. All experiments were performed in triplicate. Detailed information about the primer sequences can be found in Supplementary Materials Table S1. A heatmap was generated from real-time quantitative PCR analysis of AeIQM genes after hormone treatment. Values are the mean of three technical measurements. TBtools software (v2.027) normalized the data to obtain relative intensity values, with red indicating high expression levels and blue indicating low expression levels [38 (link)].
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2

Quantitative Analysis of VEGFA, SP1, and miR-125b-5p

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Real-time quantitative Polymerase Chain Reaction (qRT-PCR) was performed to detect the expression of VEGFA, SP1 mRNA and miR-125b-5p. Total RNA (1 μg) was reversed to cDNA by using First Strand cDNA synthesis kit (Vazyme, Nanjing, China). A total of 20 μL mixed liquid, containing cDNA, primers and enzyme mixture was added to the PCR 96-well plates for PCR reaction in PCR instrument (ABI ViiA7, United States). The PCR reaction procedure was as follows: 95°C for 30 s, then 95°C for 10 s plus 60°C for 30 s for 40 cycles. GAPDH or U6 was used as endogenous control. Primers sequences were designed as follows:

VEGFA forward: 5′-TAG​AGT​ACA​TCT​TCA​AGC​CGT​C-3′,

VEGFA reverse: 5′-CTT​TCT​TTG​GTC​TGC​ATT​CAC​A-3′;

SP1 forward: 5′-CTG​GTG​GGC​AGT​ATG​TTG​TG-3′,

SP1 reverse: 5′-AAG​CTG​GCA​GAA​CTG​ATG​GT-3′;

GAPDH forward: 5ʹ-CTC​CTC​CTG​TTC​GAC​AGT​CAG​C-3ʹ,

GAPDH reverse: 5ʹ-CCC​AAT​ACG​ACC​AAA​TCC​GTT-3ʹ;

U6 forward: 5′-ATT​GGA​ACG​ATA​CAG​AGA​AGA​TT-3′,

U6 reverse: 5′-GGA​ACG​CTT​CAC​GAA​TTT​G-3′;

miR-125b-5p forward: 5′-ACT​GAT​AAA​TCC​CTG​AGA​CCC​TAA​C-3′,

miR-125b-5p reverse: 5′-TAT​GGT​TGT​TCT​GCT​CTC​TGT​CAC-3′.

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3

Pepper Anther Total RNA Extraction and qRT-PCR

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Total RNA was isolated from pepper anthers according to the instructions of an RNA Isolation Kit (Huayueyang, Beijing, China). RNA was then reverse transcribed into cDNA using a first-strand cDNA Synthesis Kit (Vazyme). qRT–PCR was performed as described previously [24 (link)]. The primers are listed in Supplementary Data Table S1.
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4

Measurement of GAS5 Expression by qRT-PCR

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Total RNA was extracted using a TRIzol reagent (Invitrogen, Carlsbad, USA), and first-strand cDNA was synthesized using first Strand cDNA Synthesis Kit (Vazyme, Nanjing, China) according to the manufacturer’s instructions. The expression of RNA was measured by qRT-PCR (ABI PRISM7500, USA) with AceQ qPCR SYBR Green Master Mix (Vazyme, Nanjing, China). Relative expression of GAS5 was normalized with U6. The comparative Ct (ΔΔCt) method was used for quantification of gene expression. The primers used for qRT-PCR were designed and synthesized by GenePharma Co., Ltd (Suzhou, China) (Table 1).
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5

Quantitative Real-Time PCR Analysis

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Total RNA was extracted with TRIzol (Invitrogen), and 600 ng of RNA was subjected to reverse transcription using first-strand cDNA synthesis kit (Vazyme, USA) according to the manufacturer's instructions. Real-time PCR analysis was performed with ABI 7500 FAST system using the AceQ qPCR SYBR Green Master Mix Kit (Vazyme, USA), as per the manufacturer's instructions. Target mRNA levels were normalized against GAPDH level. Target mRNA expression was analyzed using the 2−ΔΔCt method (sequences shown in Table 2).
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6

Quantitative Gene Expression Analysis in BMDCs and Tumor-Draining Lymph Nodes

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BMDCs/tumor-draining lymph nodes were collected. Total RNAs were extracted by Triquick Reagent (Trizol Substitute, Solarbio, China). RNA (500 ng), quantified by NanoDrop2000 (Thermo Fisher Scientific, USA), was reversely transcribed to cDNA using the first-strand cDNA synthesis kit (Vazyme, China). Quantitative PCR was applied using the SYBR Green dye (Vazyme, China) on quant studio 3 applied biosystems (Thermo Fisher Scientific, USA). All primers were synthesized by Tsingke Biotechnology and their sequences were listed in Supplementary Table S1. The parameters of PCR assays were shown as follows: initial denaturation at 95 °C for 30 s, 40 cycles of denaturation at 95 °C for 10 s, and primer annealing and reaction at 60 °C for 30 s. Comparative quantification was assessed using the 2-ΔΔCt method with glyceraldehyde-3-phosphate dehydrogenase (GAPDH) as the endogenous control.
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7

RNA Extraction and qPCR Protocol

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RNA was extracted using TRIzol (Roche) and quantified by Biodropsis BD2000. Around 500 ng of RNA was reverse transcribed with a first-strand cDNA synthesis kit (Vazyme). qPCR was performed on ABI Step One Plus (Applied Biosystems). For miRNA qPCR, RNA samples were first polyadenylated with poly(A)polymerase and then reverse transcribed using a modified oligo-dT primer as described previously (Gu et al., 2016 (link)). Sequences for primers are listed in Table S2.
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8

Quantitative RT-PCR analysis of N. benthamiana

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The total RNA of the N. benthamiana tissue samples was extracted using the HiPure Plant RNA Mini Kit (Magen, Guangzhou, China). First-strand cDNA was synthesized using the First-Strand cDNA Synthesis Kit (Vazyme, Nanjing, China). The qRT-PCR was carried out using Hieff® qPCR SYBR Green Master Mix (Yeasen, Shanghai, China) on an Applied Biosystems Quantstudio 6 Flex system (Applied Biosystems, Foster City, CA, USA), and the relative expression levels of the assayed genes were calculated using the 2−ΔΔCt method. Each treatment had three biological replicates and three technical replicates. The primer sequences used in this study are listed in Table S3.
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9

Quantitative Analysis of Retinal Gene Expression

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RNA was isolated from retinal tissue and RGCs using a Total RNA Extractor (Sangon Biotech) and a first-strand cDNA synthesis kit (Vazyme, Nanjing, China) to reverse transcribe it into cDNA. Subsequently, RT-qPCR was performed using a universal high-specificity, dye-based, quantitative PCR detection kit (Vazyme, Nanjing, China) in an ABI 7300 sequence detection system (Applied Biosystems) with thermal cycling conditions of 94 °C for 5 min, 40 cycles of denaturation at 94 °C for 15 s, and annealing at TM value (60 °C) for 30 s. The U6 gene was selected as the reference gene, and the relative expression of the target gene was calculated by the 2-∆∆Ct method [22 (link)].
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10

Transcriptome Analysis of Ladybug Pupae

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TRIzol reagent (Invitrogen, Carlsbad, CA, United States) was used to extract total RNA from pupa of H. axyridis samples, and the RNA concentration was determined at 260 nm using a NanoDrop ONE spectrophotometer (Thermo Fisher Scientific, Waltham, MA, United States). After the total RNA (1.0 μg) was used for cDNA synthesis using the First Strand cDNA Synthesis Kit (Vazyme, Nanjing, China) with oligo (dT)18 as the primer in a 20 μL reaction system. The first-strand cDNA was used in all subsequent analyses.
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