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Sybr green 1

Manufactured by Takara Bio
Sourced in China, Japan, United States, Germany

SYBR Green I is a nucleic acid stain used to detect and quantify double-stranded DNA (dsDNA) in various applications such as real-time PCR, DNA gel electrophoresis, and DNA sequencing. It binds to the minor groove of dsDNA, resulting in a significant increase in fluorescence emission upon binding. SYBR Green I is a sensitive and cost-effective alternative to other DNA-binding dyes.

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187 protocols using sybr green 1

1

Gene Expression Profiling of ETP-ALL

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Total RNA was extracted from the leukemic cells using the RNeasy Mini Kit (Qiagen, Venio, Netherlands) according to the manufacturer’s instructions. The cDNA for reverse transcriptase (RT)-PCR was synthesized using the SuperScript First-Strand Synthesis System (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions. To compare the gene expression patterns of transcription factors related to the differentiation of myeloid and lymphoid cells in ETP-ALL with those in typical T-ALL, real-time quantitative-PCR (q-PCR) was performed on primary leukemic cells to determine the expression levels of the following transcription factors: C/EBPα and ID2, previously reported to be associated with myeloid differentiation [6 (link), 7 (link)]; NOTCH1, LYL1, IL7R and LMO2, previously reported to be associated with leukemogenesis in T-ALL [8 (link)–10 (link)]; MEF2C, PU.1, and FLT3, previously reported to be associated with myeloid and lymphoid differentiation [11 , 12 (link)].
q-PCR was conducted using the 7300 Real-Time PCR System (Applied Biosystems, Foster City, CA, USA) with SYBR Green 1 (Takara Bio, Tokyo, Japan). The relative target mRNA expression was determined using the comparative threshold (ΔCT) method. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) was used as an internal control. The primer pairs used in this study are listed in S1 Table.
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2

Quantification of Osteoclast Gene Expression

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TRIzol® reagent (Thermo Fisher Scientific, Inc.) was used to extract intracellular total RNA, and a Prime Script RT kit (Takara Bio, Inc., Otsu, Japan) was used to synthesize single-stranded cDNA. qPCR was performed using an ABI 7500 real-time PCR system (Thermo Fisher Scientific, Inc.). qPCR was conducted using cDNA (1 µl) with SYBR Green-1 (20 µl; Takara Bio, Inc.) according to the manufacturer's protocol under the following conditions: Activation at 95°C for 10 min, then 40 cycles of amplification (95°C for 10 sec, 60°C for 24 sec and 72°C for 20 sec) and a final extension at 72°C for 1 min. All the reactions were performed in triplicate and target gene expression was normalized to the reference gene β-actin. The 2−Δ∆Cq method (26 (link)) was applied to calculate the relative expression level of the target genes. The PCR products were subjected to melting curve analysis and a standard curve to confirm the correct amplification. The primers used for PCR were as follows: Cathepsin K (CTSK), forward 5′-AGAACGGAGGCATTGACTCT-3′, reverse 5′-GATGGACACAGAGATGGGTC-3′; TRAP, forward 5′-CGATCACAATCTGCAGTACC-3′, reverse 5′-ACCCAGTGAGTCTTCAGTCC-3′; nuclear factor of activated T cells cytoplasmic 1 (NFATc1), forward 5′-CGCAAGTACAGTCTCAATGG-3′, reverse 5′-CAGGTATCTTCGGTCACACT-3′; and β-actin, forward 5′-AGGCCAACCGTGAAAAGATG-3′ and reverse 5′-TGGCGTGAGCGAGACCATAG-3′.
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3

Quantitative RT-PCR Analysis of Embryonic Brain Development

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Embryos were moved from pregnant females that had been anesthetized with CO2 and placed on ice. The dorsal cerebral cortices (E14.5-PND10) were dissected, or the total telencephalon was removed (E10.5-E12.5). The tissue was immediately transferred to Trizol reagent (Invitrogen, Camarillo, CA) and processed for total RNA isolation according to the manufacturer’s protocol. Then, the total RNA was reverse-transcribed into cDNAs using a Prime Script RT reagent kit (Takara, Japan) for quantitative PCR (ABI Step One Plus, Foster City, CA) in the presence of a fluorescent dye (SYBR Green I; Takara). The relative expression of genes was determined using the 2-ΔΔct method with normalization to GAPDH expression. The primers for RT-PCR were designed based on published mouse gene sequences. The primers for Nsun5, Cdc42, RhoA, PKC, Akt and GAPDH are listed in Table 1 [29 (link), 31 (link), 55 (link)].

Primers for quantitative real-time PCR

ForwardReverse
Nsun5GAGGGAAGGGTGGATAAGGGGCACGATGCGGATGTAG
Cdc42GTTGGTGATGGTGCTGTTGCTGTGGATAACTTAGCGGTCG
RhoACATTGACAGCCCTGATAGTTTCGTCATTCCGAAGGTCCTT
PKCACCCTCGTAGAGAAGCGTGTTGAAAGTGGAGTGAAGCTG
GAPDHTGGGTGTGAACCACGAGACCACAGTCCATGCCATCAC
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4

qRT-PCR Assay for lncRNA Expression

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Primers were designed using the Pick Primers function from NCBI (http://www.ncbi.nlm.nih.gov/tools/primer-blast/) (Table S2). Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) was used as the internal control gene, the primers of which were reported in a previous study [13 (link)]. The total RNA was transcribed into cDNA using the PrimeScriptsRT reagent Kit with gDNA Eraser (TaKaRa, Dalian, China). qPCR was performed using SYBR Green I (TaKaRa, Dalian, China) with two-step reactions according to the manufacturer’s recommended protocol. The cycle threshold (2−ΔΔCt) method was used to calculate the relative expression level of lncRNA. Three replicates were run per sample and the qRT-PCR experiment was performed three times.
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5

Validating RNA-seq Findings via qPCR Assays

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The qPCR assays were performed to confirm RNA-seq results by an independent technique (Additional file 2: Table S1). The expression levels of 30 banana and 10 Foc genes were analyzed by qPCR from the RNA sampled above. The qPCR experiments were conducted on a Step One Real-Time PCR system (Applied Biosystems) using SYBR Green I (Takara, Japan). Each reaction was performed in a final volume of 20 μl, containing 10 μl of 2 × SYBR Green PCR Master Mix (Takara, Japan), 200 nM each gene-specific primer, and 50 ng cDNA template. No-template reactions were included as negative controls for each set of primers used. The thermal cycling conditions were 95 °C for 30 s, followed by 40 cycles of 5 s at 95 °C, 20 s at 58–62 °C depending on primer melting temperature, and 20 s at 72 °C, with fluorescence detection at the end of each cycle. The amplification of a single product per reaction was confirmed by melting curve analysis. All reactions were performed in technical triplicates. Banana data were normalized using two reference genes that showed little variation in the RNA-seq analysis (Actin and glyceraldehydes-3-phosphate dehydrogenase 2, GAPDH). Expression levels of fungal genes were given in relation to the fungal β-actin and IF3b (transcription initiation factor) genes. Primers used in these experiments were designed by Primer Premier 6.0 software.
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6

Cyclin D1 mRNA Expression in HCC

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Real-time RT-PCR was performed to measure the cyclin D1 mRNA levels in HCC cells as described previously [39 (link)]. Briefly, total RNA was isolated from the HCC cells using a RNeasy mini kit (Qiagen) according to the manufacturer's instructions, and reversely transcribed to cDNA using MMLV reverse transcriptase and the oligo(dT) primer kit (Solgent). Actin was used as the control gene. Real-time PCR was performed using SYBR Green I (Takara) and a Light-Cycler rapid thermal cycler (Roche Diagnostics). The primer sequences are shown in Supplementary Table 3. The relative VRK1 levels in HCC cells were determined using the 2−ΔΔCT method, as described [40 (link)].
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7

Quantifying miR-192-5p and ALX1 mRNA

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We extracted total RNA using the TRIzol reagent (Thermo Fisher Scientific, Inc.). Small RNAs were purified using the mirVana miRNA isolation kit (Thermo Fisher Scientific, Inc.). The relative expression level of miR-192-5p was measured using the TaqMan microRNA assays (Applied Biosystems; Thermo Fisher Scientific, Inc.). Semi-quantitative PCR with SYBR green I (Takara Biotechnology co., Ltd.) was used to compare the relative expression of ALX1 mRNAs using the SYBR® Premix Ex TaqTM Kit (Takara Biotechnology co., Ltd.).
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8

Comet Assay Protocol for DNA Damage

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A comet assay was performed using a CometAssay Kit (Trevigen, Gaithersburg, MD, USA) according to the manufacturer’s protocol. Briefly, GS cells were cultured for 2 weeks after adenovirus infection and suspended in PBS (2 × 105 cells/ml). The cell suspension was mixed with CometAaay LM Agarose (Trevigen) at a ratio of 1:10, and 50 μl was transferred to a CometSlide (Trevigen) for immobilization. After incubation in lysis solution, cells were treated with an alkaline solution for 30 min followed by electrophoresis. DNA was stained with SYBR Green I (TaKaRa Bio, Otsu, Japan). DNA damage was quantified by measuring the length of the visible comet tail. Cells with a ratio greater than or equal to 2 were counted as positive for DNA damage. Figures show the percentage of cells positive for DNA damage per treatment.
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9

Quantitative PCR Analysis of IDH1 Expression

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The purified DNA finally produced by CHIP was used as template DNA for the PCR reaction. qPCR analysis was performed using SYBR-Green I (Takara Bio, Inc., Kusatsu, Japan). GAPDH was used as an endogenous control. The primers used in this study were provided by Realgene (Realgene, Nanjing, China) (Supplementary Table S2): IDH1 forward, 5’-AGGTGGGCTGAGGAGGC-3’ and reverse, 5’-ACAGGGTAGGTCCGAGCTTT-3’; GAPDH forward, 5’-GAAGGTGAAGGTCGGAGTC-3’ and reverse, 5’-GAAGATGGTGATGGGATTTC-3’. Finally, the period threshold (Ct) value was analyzed by the 2−ΔΔCt method. Each individual experiment was performed a total of three times.
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10

Quantifying Gene Expression in Cells

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Total RNA was extracted with Trizol reagent (Invitrogen) according to the manufacturer's protocol and 2 μg was reversed‐transcribed using the GoScript™ Reverse Transcription system (Promega, Madison, WI, USA). For real‐time quantitative PCR, the iQ5 system (Bio‐Rad, Hercules, CA, USA) with SYBR Green I (Takara, Kusatsu, Japan) was used. Amplification was performed at 95°C for 5 minutes, 95°C for 45 seconds and 57°C for 45 seconds of each step for 45 cycles. The housekeeping gene GAPDH was used as a control. The primers used are shown below: Tumour necrosis factor‐α (TNF‐α): Forward, tcttctcattcctgcttgtgg; Reverse, ggtctgggccatagaactga; inducible nitric oxide synthase (iNOS): Forward, gggctgtcacggagatca; Reverse,ccatgatggtcacattctgc; arginase‐1 (Arg‐1):Forward, aaagctggtctgctggaaaa; Reverse, acagaccgtgggttcttcac.
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