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13 protocols using nucleozol reagent

1

Quantifying Gene Expression in Ovarian Cancer

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Subconfluent parental human epithelial ovarian cancer lines OVCAR8 and SKOV3 and cisplatin-resistance human epithelial ovarian cancer cell lines OVCAR8CR and SKOV3CR were treated with various conditions for 48 h. Total RNA was isolated from treated cells by using the NucleoZOL reagent (Takara Bio USA Inc) and subjected to reverse transcription (RT) reactions with hexamer, M-MuLV reverse transcriptase (New England Biolabs, Ipswich, MA), and dNTPs (GenScript USA Inc. Piscataway, NJ, USA). RT products were used as qPCR templates. The qPCR primers for the genes of interest were designed by using the Primer3 Plus program (Table S1). TqPCR reactions were carried out by using SYBR Green-based Forget-Me-Not™ qPCR Master Mix (Biotium Inc., Hayward, CA, USA) on a CFX-Connect unit (Bio-Rad Laboratories, Hercules, CA, USA) as described.42 (link),49 , 50 (link), 51 (link), 52 (link), 53 (link)
GAPDH was used as a reference gene. Relative expression was calculated by using the 2−ΔΔCt method. All qPCR reactions were done in triplicate.
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2

Quantifying miRNA and mRNA Transcripts in Cells

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At the endpoint, the transfected cells were subjected to total RNA isolation by using NucleoZOL Reagent (Takara Bio USA, Mountain View, CA) according to the manufacturer’s introduction. For qPCR analysis of mRNA transcripts, total RNA was used for reverse transcription with the hexamer and M-MuLV (NEB). The cDNA products were diluted as templates for qPCR. The qPCR primers were designed by Primer3 Plus program (48 (link)). For assessing the miR expression levels mediated by the three expression systems, the reverse transcription reactions were carried out by using miR-specific reverse primers that were complementary with the 3’-end six nucleotides of mature miR-5p and/or miR-3p, preceded with a 44-nt artificial stem-loop sequence. SYBR Green-based quantitative real-time PCR analysis was performed by following our previously optimized TqPCR protocol (49 (link)). The qPCR reactions were done in triplicate. All expression values were normalized to the reference gene GAPDH expression by using the 2–ΔΔCt method (50 –53 (link)). The sequences of the qPCR primers are listed in Supplemental Table 1.
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3

Quantitative RT-PCR Analysis of Gene Expression

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Total RNA was extracted from tissue samples using NucleoZOL Reagent (Takara, Dalian, China) according to the manufacturer’s protocol, and cDNA was synthesized from 1 µg of total RNA using a PrimeScript® 1st strand cDNA Synthesis Kit (Takara, Dalian, China) in a final reaction volume of 20 µl. Quantitative RT-PCR was performed using SYBR Premix Ex Taq (Takara, Dalian, China) with primers listed in Table 1. The expression levels were normalized to the GAPDH mRNA level for each sample obtained from parallel assays, and the data were analyzed according to the relative 2^ (-ΔΔCt) method.
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4

qPCR Analysis of mRNA and miRNA Expression

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At the endpoint, the transfected cells were subjected to total RNA isolation by using NucleoZOL Reagent (Takara Bio USA, Mountain View, CA) according to the manufacturer’s introduction. For qPCR analysis of mRNA transcripts, total RNA was used for reverse transcription with the hexamer and M-MuLV (NEB). The cDNA products were diluted as templates for qPCR. The qPCR primers were designed by Primer3 Plus program [48 (link)]. For assessing the miR expression levels mediated by the three expression systems, the reverse transcription reactions were carried out by using miR-specific reverse primers that were complementary with the 3′-end six nucleotides of mature miR-5p and/or miR-3p, preceded with a 44-nt artificial stem-loop sequence. SYBR green-based quantitative real-time PCR analysis was performed by following our previously optimized TqPCR protocol [49 (link)]. The qPCR reactions were done in triplicate. All expression values were normalized to the reference gene GAPDH expression by using the 2–ΔΔCt method [50 (link)–53 (link)]. The sequences of the qPCR primers are listed in Supplemental Table 1.
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5

Quantitative RT-PCR Analysis of Endometrial Tissue

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Total RNA was extracted from endometrial tissues, HEC-1A, and Ishikawa cells using NucleoZOL reagent (Takara) according to the manufacturer’s instructions. Complementary DNA was synthesized using Moloney murine leukemia virus reverse transcriptase (MMLV-RT, Promega) and random hexamers (BioFact). Quantitative real-time reverse transcription PCR (qRT-PCR) analysis was performed in triplicates using the SYBR green real-time PCR master mix reagent (Biofact) and QuantStudio 3 Real-time PCR System (Life Technologies Inc.). Relative mRNA expression was calculated from the comparative threshold cycle (Ct) values relative to human GAPDH. The following primers were used—GAPDH: forward 5′-TTGCCATCAATGACCCCTTCA-3′, reverse 5′-CGCCCCACTTGATTTTGGA-3′; Cyclophilin: forward 5′-GCAAAGTGAAAGAAGGCA-3′, reverse 5′-CCATTCCTGGACCCAAAG-3′; SESN2: forward 5′-ACTGCGTCTTTGGCATCAG-3′, reverse 5′-CTTCTCTGAGTGGCGGAAGT-3′; MKI67: forward 5′-ACGCCTGGTTACTATCAAAAG-3′, reverse 5′-CAGACCCATTTACTTGTGTTGGA-3′; CDKN1A: forward 5′-TGTCCGTCAGAACCCATGC-3′, reverse 5′-AAAGTCGAAGTTCCATCGCTC-3′; and CDKN1B: forward 5′-AACGTGCGAGTGTCTAACGG-3′, reverse 5′-CCCTCTAGGGGTTTGTGATTCT-3′.
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6

Comprehensive RNA Isolation from Diverse Murine Tissues

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For total RNA isolation, mouse brain, fat (inguinal region), heart, kidney, liver, lung, muscle, spleen, femur and parietal bone (PB) at various ages were harvested immediately after sacrificing the animals, placed in RNase-free mortars containing NucleoZOL Reagent (Takara Bio USA, Mountain View, CA) and liquid nitrogen, and crashed with RNase-free pestles in a RNase-free biosafety cabinet. Total RNA was subsequently isolated according to the manufacturer's introduction, and subjected to reverse transcription with hexamer and M-MuLV (New England Biolabs, Ipswich, MA). The cDNA products were diluted as templates for qPCR.
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7

Quantification of mRNA and miRNA by Touchdown qPCR

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Total RNA was extracted by using the NucleoZOL Reagent according to the manufacturer’s instructions (Takara Bio USA, Mountain View, CA). To synthesize the cDNA for mRNA or mature miRNA quantification, random hexamer, the miRNAs’ specific stem-loop primers, and the reverse primer of Gapdh were incubated together with total RNA at 70°C for 5 min and then reverse transcribed with M-MuLV Reverse Transcriptase (New England Biolabs). The resultant cDNA products were diluted 10- to 50-fold and used as templates for touchdown qPCR (TqPCR). PCR primers were designed by Primer3 Plus program (Table S1). The TqPCR analysis was carried out with our optimized TqPCR protocol40 (link) using the 2× SYBR Green qPCR master mix (Bimake, Houston, TX). A typical TqPCR program was as follows:40 (link) 95°C × 3 s for one cycle; 95°C × 20 s, 66°C × 10 s, for 4 cycles by decreasing 3°C per cycle; and 95°C × 20 s, 55°C × 10 s, 70°C × 1 s, followed by plate read, for 40 cycles. Each assay condition was performed in triplicate. All sample values were normalized to Gapdh expression by using the 2–ΔΔCt method as described.41 (link), 42 (link), 43 (link)
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8

Quantitative Real-Time PCR Analysis of Gene Expression

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Subconfluent iMAD cells were infected with the indicated adenoviruses. At the indicated time points, total RNA was isolated by using NucleoZOL Reagent (Takara Bio USA, Mountain View, CA) according to the manufacturer's introduction and subjected to reverse transcription with a hexamer and M-MuLV Reverse Transcriptase (New England Biolabs, Ipswich, MA). The resultant cDNA products were diluted 50-folds and used as templates for TqPCR. PCR primers were designed by Primer3 Plus program (Supplemental Table 1). The touchdown-quantitative PCR analysis was carried out by our optimized TqPCR protocol65 (link) using the 2 × SYBR Green qPCR master mix (Bimake, Houston, TX). All sample values were normalized to Gapdh expression by using the 2–ΔΔCt method as described.7 (link), 8 (link)
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9

Osteogenic Differentiation Evaluation

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CK was provided by Zhejiang Hongguan Bio-pharma Co., Ltd., and dissolved in DMSO, and diluted in PBS. Modified Eagle’s Medium of Alpha (α-MEM), Dulbecco’s Modified Eagle Medium/Nutrient Mixture F-12 (DMEM/F-12), fetal bovine serum (FBS), and penicillin/streptomycin were purchased from Gibco (United States). Beta-glycerolphosphate, dexamethasone, ascorbic acid phosphate, Safranine O, and Fast Green were purchased from Sigma (United States). Alizarin Red S was purchased from Solarbio (Beijing, China). Cell Counting Kit-8 (CCK-8) was purchased from Beyotime (Beijing, China). NucleoZOL reagent, Reverse Transcription Kit and SYBR-Green Master Mix were supplied by Takara (Japan). Hematoxylin-eosin (H&E) was purchased from biosharp (China). Primary antibodies against CD31, β-catenin, and DAPI were supplied by Santa Cruz Biotechnology (United States); Primary antibodies anti-CTSK, anti-ALP, anti-OPG, anti-RANKL, anti-Runx2, and anti-OPN were purchased from Bioss (China); Anti-GAPDH, and DAPI were obtained from Abcam (United States). Secondary antibodies HRP-conjugated Goat Anti-Rabbit IgG, Goat anti-Mouse IgG (H + L), Rabbit Anti-Rabbit IgM/Cy3 and Rabbit Anti-Mouse IgM/FITC were obtained from Bioss (China). Dual-Luciferase Reporter Assay System was supplied by Promega Company (United States). Matrigel was purchased from Becton Dickinson (United States).
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10

Gene Expression Analysis by qPCR

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Subconfluent cells were treated with various conditions for 48h. Total RNA was isolated by using the NucleoZOL reagent (Takara Bio USA Inc.), and subjected to reverse transcription (RT) reactions as previously described [63 (link)–66 (link)]. The RT cDNA products were used as PCR templates. The primers for the genes of interest were designed by using Primer3 Plus program (Supplementary Table 1). TqPCR reactions were carried out by using SYBR Green-based Forget-Me-Not™ qPCR Master Mix (Biotium Inc., Hayward, CA) on a CFX-Connect unit (Bio-Rad Laboratories, Hercules, CA) as described [67 (link)–70 (link)]. Relative gene expression was normalized to GAPDH by using the 2−∆∆Ct method. All qPCR reactions were done in triplicate.
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