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Abi steponeplus system

Manufactured by Thermo Fisher Scientific
Sourced in United States, United Kingdom, China, Japan, Switzerland

The ABI StepOnePlus system is a real-time PCR instrument designed for a wide range of applications. It provides accurate and reliable results for gene expression analysis, genotyping, and other molecular biology applications.

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289 protocols using abi steponeplus system

1

RT-qPCR for mRNA and miRNA Analysis

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Total RNA was extracted by Trizol reagent (Invitrogen) and then was used to synthesize cDNA by Moloney murine leukemia virus reverse transcriptase (New England BioLabs) with an oligo (dT)18 primer. According to the manufacturer's protocol (Applied Biosystems), the cDNAs were amplified with primers listed in the Supplementary Table S1 using an ABI StepOne Plus system with SYBR Green Master Mix for mRNA detection [43 (link)]. For detection of mature miRNAs, cDNA synthesis was carried out by MultiScribeTM Reverse Transcriptase system and then quantitative miRNA real-time PCR was performed by the ABI StepOne Plus system (Applied Biosystems) [42 (link)].
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2

Genotyping of Seven NAT2 SNPs

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Seven SNPs were selected in this study, that is, NAT2 rs1799929, rs120, rs1041983, rs1801280, rs1799930, rs1799931, and rs1801279. Date collection was conducted utilizing the Sequence Detection Software on an ABI StepOnePlus System (Thermo Fisher Scientific, Waltham, MA, USA). TaqMan primers and probes were designed using the ABI Assay-by-Design custom service. Samples were performed in triplicate and averaged. Genotyping results were validated by repeating once more. Amplification conditions on ABI StepOnePlus were as follows: 95°C for 10 minutes, followed by 40 cycles at 95°C for 15 seconds, and at 60°C for 60 seconds. The completed PCR plates were read with the ABI software. Laboratory personnel were blinded to the case-control status. NAT2 alleles were identified according to the Human NAT2 Alleles (Haplotypes) (http://nat.mbg.duth.gr/Human%20NAT2%20alleles_2013.htm).
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3

Quantitative Real-time PCR Analysis of Lipid Metabolism Genes

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Total RNA was extracted from mouse tissues using TRIzol reagent (Thermo Fisher Scientific Inc. Waltham, MA) and the first-strand cDNA was synthesized from 2.0 μg mRNA using High-Capacity RNA-to-cDNA™ Kit (Thermo Fisher Scientific Inc. Waltham, MA). Real-time PCRprimers for mouse H6PDH (F: 5′-TGGCTACGGGTTGTTTTT GAA-3′; R: 5′-TATACACGGTACATCTCCTCTTCCT-3′), 11β-HSD1 (F: 5′-CCTTGGCC-TCATAGACACAGA AA C-3′; R: 5′-GGAGTCAAAGGCGATTTGTCAT-3′), ACC (F: 5′-TGT AAATCTGGCTGCATCCATTAT-3′; R: 5′-TGGTAGACTGCCCGTGTGA-3′), ATP-citrate lyase (ACL) (F: 5′ -ATGCCAAGACCATCCTCTCACT-3′; R: 5′-TCTCACAATGCCCTTGAAGGT-3′), HSL (F: 5′-GGGCAAAGAAGGATCGAAGAA-3′; R: 5′ GCGTAAATC CATGCTGTGTGA-3′), ATGL (F: 5′-TCGTGGATGTTGGTGGAGCT-3′; R: 5′-TGTGGCCTCATTCCTCCTA-3′) , C/EBPα (F: 5′-TGGACAAG AACAGCAACGAGTAC-3′; R: 5′-CGGTCATTGTCACTGGTCAACT-3′), and C/EBPβ (R:5′-CTGCGGGGTTGTTGATGT-3′; R: 5′-ATGCTCGAAACGGAAA GGT-3′) were designed by Primer express software 2.0 (Thermo Fisher Scientific Inc. Waltham, MA). Quantitative Real-time PCR analysis was performed with SYBER green kit following manufacturer’s protocol in the ABI StepOne Plus System (Thermo Fisher Scientific Inc. Waltham, MA). Threshold cycle (Ct) readings for each of the unknown samples were then used to calculate the amount of target genes. The expression for target genes was normalized to the 18S rRNA values.
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4

SNP Genotyping in Chinese Han

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We reviewed the HapMap data and picked out frequent SNPs (frequency >5% in the Chinese Han people). Five SNPs (rs6214, rs6218, rs35767, rs5742612, and rs5742714) were genotyped and evaluated. Sequence Detection Systems software on an ABI StepOnePlus system (Thermo Fisher Scientific) was used for data collection and analyses. Primers and probes for TaqMan assays were designed online on the ABI Assay-by-Design services. We used 384-well plates from ABI, and all samples were run in triplicate. Two technicians independently performed SNP genotyping in a blinded manner. The amplification conditions were two minutes at 50°C and 10 minutes at 95°C, followed by 40 cycles at 95°C for 15 seconds and at 60°C for 60 seconds.
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5

Quantification of Neuroactive Metabolites

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Trp, 5-hydroxytryptamine (5-HT), kynurenine (Kyn) and quinolinic acid (Quin), and LPS (Escherichia coli, serotype 0111:4) were purchased from Sigma-Aldrich (St. Louis, MO, USA). Benzoyl chloride and ammonium formate were obtained from Aladdin (Shanghai, China). LC-MS grade methanol, acetonitrile, and formic acid were purchased from Fisher Scientific. Enzyme-linked immunosorbent assay (ELISA) kits were purchased from Boster Biological Technology Co., Ltd. (Wuhan, China). NMDAR antibody was purchased from Abcam (Cambridge, UK). The real-time PCR system used in this study was the Thermo Fisher ABI StepOne Plus system. Ultra-high-performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) analysis was performed on an Agilent 1290 Infinity II UHPLC system coupled to a 6470A triple quadrupole mass spectrometer (Santa Clara, CA, United States).
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6

Quantitative RT-PCR Analysis of FGFR1

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RNA was extracted using the RNeasy Mini Kit (Qiagen, Germantown, MD), and cDNA was synthesized using the SuperScript VILO cDNA Synthesis Kit (Thermo Fisher, Richardson, TX). Real-time PCR was performed by using the ABI StepOnePlus system (Thermo Fisher) and iTaq™ Universal SYBR Green Supermix (Bio-Rad, Hercules, CA). For data analysis, the 2−ΔΔCT method was used to calculate the fold changes. GAPDH expression was considered to be unaffected under our treatment conditions and was used as a reference gene. The primer sequences used for real-time PCR were as follows (5′-3′): FGFR1, forward, CCCGTAGCTCCATATTGGACA, and reverse, TTTGCCATTTTTCAACCAGCG; GAPDH, forward, GAAGGTGAAGGTCGGAGTC, and reverse, GAAGATGGTGATGGGATTTC. Each experiment was run in triplicate, and the error bars represent the range of the fold changes calculated from three or four independent experiments.
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7

Quantitative Gene Expression Analysis in Zebrafish

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For each time point, A total of 15 to 20 fish were separated into 2 tubes equally. Here, the sample size estimate is based on our previous studies. Trizol (Invitrogen) was immediately added to each tube. Then, total RNA was isolated from zebrafish larvae by Trizol (Invitrogen) according to the manufacturer's protocol. Total RNA quantities were measured by a Nanodrop spectrometer (Nanodrop 2000). Five hundred nanograms of total RNA was reverse transcribed using HiScript II Q RT SuperMix for qPCR (+gDNA wiper) (vazyme) according to the manufacturer's protocol. Two microliters of RT product (1:10 diluted) and 10 μL of SYBR Green Master Mix (vazyme) were used in qPCR on an ABI StepOne Plus System (Thermo Fisher) according to the manufacturer's protocol. The specificity of PCR was checked by melting curve analysis. In every qPCR assay, eef1a1 was used as the control gene for any significant bias of starting materials across samples. Primers used in this study were listed in Table L in S2 Data.
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8

Transcriptome Analysis of Breast Cancer Cells

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Total RNA from 3 passages (3 biological replicates) each of MCF-7, MCF7-RES, MDA-MB-231 and MDA-RES cells was purified using the RNAiso™ Plus Kit (TaKaRa, Japan). After RNA purification and DNase I digestion, ribosomal RNAs (rRNAs) were removed from total RNA with the RiboMinus Eukaryote Kit (Qiagen, Valencia, CA). The remaining RNAs were fragmented and used to synthesize cDNAs, followed by end repairing and adenine connection. Then the sequencing adaptors were ligated to the fragments and those with suitable sizes were selected for PCR amplification. An ABI StepOnePlus System (ThermoFisher Scientific, Massachusetts, USA) and an Agilent 2100 Bioanaylzer (Agilent Technologies, California, USA) were used to quantify and qualify the sample libraries in the quality control steps. Finally, all the libraries were sequenced by an Illumina HiSeqTM 2000 sequencer.
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9

RNA Extraction and qRT-PCR Analysis

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TRIzol reagent (Invitrogen) was used to extract total RNA from cells or tissues as the manufacturer’s instructions. The total RNA was then reversely transcribed into cDNA using PrimeScript RT Master Mix (TaKaRa, Japan). The SYBR Green PCR kit (TaKaRa, Kyoto, Japan) was employed to conduct qRT-PCR with ABI StepOne Plus system (Thermo Fisher Scientific, USA). GAPDH and U6 were adopted as internal controls. 2−ΔΔCT method was used to calculate the relative expression. The sequences of primers are listed in Supplementary Table S2.
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10

Quantifying HER-2 Expression in Breast Cancer Cells

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HER-2 levels were measured using one-step HER-2 TaqMan RT-qPCR kits (Suzhou GenePharma Co., Ltd.), the fluorophore (SYBR Green) was purchased from Thermo Fisher Scientific, Inc. Reactions contained 2.5 µl 10× PCR buffer, 2.5 µl 5× RT buffer, 0.375 µl of each primer, 0.5 µl of each probe, 0.5 µl enzyme mix, and 8 µl blood RNA extract in 20 µl. Total RNA from MDA-MB-231 cells (from the American Type Culture Collection, Manassas, VA, USA) were used as the negative control. RT-qPCR cycling was performed on an ABI-Step One Plus system (Thermo Fisher Scientific, Inc.) as follows: 45°C for 5 min, 95°C for 30 sec, and 40 cycles of 5 sec at 95°C and 50 sec at 62°C. Fluorogenic signals were detected at the end of the annealing-extension steps. A threshold was automatically set and the threshold cycle value (Cq) was determined (25 (link),26 (link)). Two replicate assays within and between runs were performed. The sequences of the primers used for HER-2 were as follows: Forward, 5′-CCAGCTGGCTCTCACACTG-3′; and reverse, 5′-AGCCCTTACACATCGGAGAAC-3′; probe, 5′-FAM/AGGCCCGAGAGCGGTTGGTGT/BHQ1-3′. Sequences of the primers used for β-actin were as follows: Forward, 5′-GACCCAGATCATGTTTGAGACCTT-3′; and reverse, 5′-CCATCACGATGCCAGTGGTA-3′; probe, 5′-FAMCCATGTACGTTGCTATCCAGGCTGTGCBHQ1-3′.
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