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8 protocols using rnase free h2o

1

RT-PCR and qRT-PCR for Gene Expression

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Total RNA was extracted from target tissues using Trizol reagent (Invitrogen, Carlsbad, CA, USA), following the manufacturer’s protocol. Reverse transcription was performed using the Quant cDNA Synthesis Kit (Tiangen, Beijing, China) with 1 µg of unpurified total RNA as a template in a 20 μL total volume.
RT-PCR (Promega, Madison, WI, USA) was used to assess the temporal and spatial expression profiles of LmigCSPIII. Primers used are shown in Table 1. The thermal cycling conditions for RT-PCR were as follows: 45 min at 45 °C and 3 min at 95 °C; followed by 30 cycles of 30 s at 95 °C, 30 s at 55 °C and 45 s at 68 °C. The reaction was completed with 10 min at 68 °C.
Both RT-PCR and qRT-PCR were used to determine RNA interference efficiency. Primers for qRT-PCR were specifically designed (Table 1). The actin gene was used as an endogenous control to correct for sample-to-sample variation. The 20 μL reaction system included 10 μL SuperReal PreMix SYBR Green (Tiangen, Beijing, China), 0.6 μL qRT-PCR Sense Primer, 0.6 μL qRT-PCR Antisense Primer, 1 μL synthesized cDNA, 2 μL ROX and 5.8 μL RNase-free H2O (Tiangen). The thermal cycling conditions for qRT-PCR were 15 min at 95 °C; followed by 40 cycles of 10 s at 95 °C, 20 s at 58 °C and 31 s at 72 °C. Each sample reaction was repeated three times and the results were averaged.
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2

DNA and RNA Extraction from Blood and Tissues

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Genomic DNA was extracted from venous blood using the standard phenol/chloroform method. The concentration and purity of the genomic DNA were measured using Nanodrop (Thermo Scientific, USA). Tris-EDTA buffer was added to the DNA samples to produce a final concentration of 100 ηg/μL. The DNA samples were maintained at −20°C until use.
Total RNA was extracted from the liquid nitrogen-frozen tissues described above, using Trizol reagent (Invitrogen, USA). After being extracted, total RNA was treated with RNase-free H2O (Tiangen, China). The concentration of the extracted RNA was measured using the Nanodrop2000 (Thermo Scientific, USA). First-strand cDNA was synthesized from 1 μg of total RNA using the PrimeScript1 RT Reagent Kit (Perfect Real-Time) (TaKaRa, Biotechnology Co. Ltd., Dalian, China). The reactions were performed under the following conditions: 42°C for 2 min, 37°C for 15 min, and 85°C for 5 sec. The reactions were then stored at 4°C as described in the manufacturer's instructions.
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3

Gene Expression Analysis by qPCR

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Total RNAs were extracted from cells by a TRIzol reagent (Invitrogen), and the quality and concentration were evaluated for optical density 260/280 ratio using a Nanodrop 2000 spectrophotometer, and reverse transcriptions were performed by the PrimeScript™ RT Reagent Kit with the gDNA Eraser Kit (TaKaRa Biotechnology, Tokyo, Japan), following the manufacturer’s instructions. qPCR primers (Table 2) were designed by Primer Premier 5 software. The reaction system was 10 μL, including 5 μL of SYBR Green Premix Ex Taq (TaKaRa), 3μL of RNasefree H2O (Tiangen, Beijing, China), 0.5 μL of forward primer, 0.5 μL of reverse primer, and 1 μL of cDNA. The reaction conditions were as follows—95 °C for 3 min, followed by 95 °C for 10 s, the primer-specific annealing temperature for 20 s, and 72 °C for 20 s; these were then repeated 40 times. The β-actin gene was used as an internal control. Each sample was assayed in triplicates.
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4

Spatial-Temporal Expression of PPP3CA in Goat Muscles

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Total RNAs of five muscle tissues were extracted. RT-qPCR was used to analyze the relative mRNA expression of PPP3CA gene in different muscle tissues of Tianfu goat at 150 days old. Analysis of spatial-temporal expression patterns of PPP3CA gene used the housekeeping gene, GAPDH gene as an internal control. The primers are shown in Table 1. The 25 μL reaction system of RT-qPCR was: 12.5 μL SYBR premix Ex TAq™ (TaKaRa), 1 μL Forward primer (4.19 nmol per OD), 1 μL Reverse primer (4.37 nmol per OD), 2 μL cDNA of each muscle tissue, 8.5 μL RNase-free H2O (Tiangen). RT-qPCR program initially started with: 95 °C for 10 s followed by 40 cycles of 95 °C for 5 s and 60 °C for 30 s.
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5

Quantitative Real-Time PCR Protocol

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Synthesized cDNA libraries were diluted with RNase-free water (Tiangen, Beijing, China) at a ratio of 1:3 before qRT-PCR. The qRT-PCR reaction system was 10 µL, including 5 µL of SYBR Green Premix Ex Taq (TaKaRa), 3µL of RNasefree H2O (Tiangen), 0.5 µL of forward primer, 0.5 µL of reverse primer, and 1 µL of cDNA. In addition, qRT-PCR reaction conditions were as follows, 95℃ for 3 min, followed by 95℃ for 10 s, the primer-specific annealing temperature for 20 s, and 72℃ for 20 s; these were then repeated 40 times. GAPDH, β-actin, and U6 (for miRNA) were used as the internal control. All relative gene expression levels were collected with CPX Connect Real-Time System (Bio-Rad, Hercules, CA). The 2−ΔΔCt method was used to calculate qRT-PCR data. Each sample was assayed in triplicates.
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6

qRT-PCR Quantification of Gene Expression

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For qRT-PCR, first-strand cDNA was synthesized from 1 μg of total RNA using the PrimeScript RT Reagent Kit (Perfect Real-Time) (TaKaRa, Biotechnology Co. Ltd., Dalian, China). The reactions were performed under the following conditions: 42°C for 2 min, 37°C for 15 min and 85°C for 5 s.
qRT-PCR was conducted with two pairs of primers designed with Primer Premier 5 software (Table 2). GAPDH was chosen as the housekeeping gene for normalization. An 11 μL reaction containing 6 μL of SYBR premix Ex TaqTM (TaKaRa, Biotechnology Co. Ltd., Dalian, China), 1 μL of cDNA, 0.5 μL of forward primer, 0.5 μL of reverse primer and 3 μL of RNase-free H2O (Tiangen, Beijin, China) was used for qRT-PCR. The reactions were carried out with the following amplification conditions: 95°C for 10 s followed by 40 cycles of 95°C for 5 s and 60°C (or the appropriate annealing temperature) for 30s. Each sample was run in 3 technical replicates. The 2ΔΔCt method was applied to quantify mRNA expression levels.
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7

Quantifying Gene Expression in Plants

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Transcriptional levels of HgNR, HgNiR, HgGS, HgGDH, and HgAS were analyzed by RT-qPCR using the 18s gene as an internal control with the primers shown in Table 3. Total RNA was extracted from roots, leaves, and fruits using RNAiso Plus (TaKaRa), and treated with RNase-free H2O (Tiangen) according to the instructions by the manufacturer. Data were analyzed using Opticon Monitor software (Bio-Rad). Three technical replicates for one of the three biological replicates were performed for each gene. The 2–ΔΔCt method was used to analyze mRNA expression levels [48 (link)].
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8

Myoz3 Gene Expression by RT-qPCR

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Expression pattern of Myoz3 gene was detected by RT-qPCR (real-time quantitative PCR). Based on cloning results, two pairs of primers were designed with Primer Premier 5 (Table 2). GAPDH was chosen as the housekeeping gene for normalization. An 11 μL reaction system containing 6 μL of SYBR premix Ex TAq™ (Takara), 1 μL of cDNA, 0.5 μL of forward primer, 0.5 μL of reverse primer, and 3 μL of RNase-free H2O (Tiangen) was used for RT-qPCR. Reaction was carried out using the PCR touch T960 (Hangzhou Jingle Scientific instrument Co., Ltd.) with the following amplification conditions: 95°C for 10 s followed by 40 cycles of 95°C for 5 s and 60°C for 30 s. Each sample was run in 3 duplicates. The 2−ΔΔCt method was applied to analyze Myoz3 mRNA expression.
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