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Abi 7500 fast sequence detection system

Manufactured by Thermo Fisher Scientific
Sourced in United States, Switzerland, Spain

The ABI 7500 Fast Sequence Detection System is a real-time PCR instrument designed for gene expression analysis and quantitation. The system utilizes TaqMan chemistry and provides fast, sensitive, and reliable results for a variety of applications.

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56 protocols using abi 7500 fast sequence detection system

1

Real-Time qPCR Analysis of Inflammatory Markers

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At 3 and 7 days explants were processed as reported above to extract RNA and synthesize cDNA. Transcribed products were analyzed using commercially available master mix and the appropriate target probes (IL-6: Rn01410330_m1, IL-1β: Rn00580432_m1, iNOS: Rn00561646_m1, TNF-α: Rn01525859_g1) on an ABI 7500 Fast Sequence Detection System (Applied Biosystems, Foster City, CA).
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2

RNA Extraction and RT-qPCR for HIF-1α and ADRP Expression

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The cells were dissolved in TRIzol reagent (Invitrogen; Thermo Fisher Scientific, Inc.), and total RNA was extracted, according to the manufacturer's protocol. Total RNA (1 µg) was converted into 1 µg cDNA using an M-MLV reverse-transcription system (Invitrogen; Thermo Fisher Scientific, Inc.) in the presence of oligo (dT)18 (Beijing TransGen Biotech Co., Ltd.). Reverse transcription-quantitative (RT-q)PCR was performed using an ABI-7500 Fast Sequence Detection system (Applied Biosystems; Thermo Fisher Scientific, Inc.) with SYBR® Green PCR mix (Beijing TransGen Biotech Co., Ltd.). The reaction system contained 10 µl 2X SYBR® Green PCR Master mix (Beijing TransGen Biotech Co., Ltd.), 4 pmol of each primer (Sangon Biotech Co., Ltd.) and 0.2 µl RT reaction product. The samples were set in triplicate. The thermocycling parameters were as follows: 95°C for 10 min, followed by 40 cycles of 95°C for 15 sec and 60°C for 30 sec, and a detection step at 72°C for 30 sec. The specific gene primers were as follows: HIF-1α forward, 5′-AGG TGG ATA TGT CTG GGTTG-3′, HIF-1α reverse, 5′-AAG GAC ACA TTC TGT TTG TTG-3′; ADRP forward, 5′-GGC TAG ACA GGA TTG AGG AGAG-3′, and ADRP reverse, 5′-TCA CTG CCC CTT TGG TCTTG-3′. The relative abundance of the HIF-1α and ADRP transcript was quantified using the comparative Cq method (15 (link)), with β-actin as an internal control.
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3

Quantitative Analysis of miRNA Expression in PTC

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Serums of PTC patients were obtained from Fujian Medical University Union Hospital after surgical resection. Serums of PTC patients were obtained from Fujian Medical University Union Hospital. The study protocol was approved by the Institute Research Ethics Committee at Fujian Medical University Union Hospital. Total RNA was extracted from the serum and cell using Trizol (Invitrogen). cDCA was reverse‐transcribed using the TaqMan MiRNA Reverse Transcript Kit (Applied Biosystems). miRNAs were quantified using SYBR Premix Ex TaqTM (TaKaRa) by ABI 7500 Fast Sequence Detection System (Applied Biosystems Prism) and the relative expression using the 2‐ΔΔCT method. U6 forward, 5′‐AGAGCCTGTGGTGTCCG‐3′, reverse, 5′‐CATCTTCAAAGCACTTCCCT‐3′.
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4

miRNA Expression Analysis in Lung Cancer

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In order to determine the expression levels of miRNA, tissues were obtained from patients who had undergone resection for lung cancer. Besides cancer tissues, apparently non-affected tissue was also collected from each patient and used as paired control. In all patients, comparable control tissues were processed for histological examination. Total RNAs were extracted by Trizol method, and then were reverse transcribed with TaqMan Reverse Transcription Kit and assayed by the respective TaqMan microRNA kit (Applied Biosystems, Forster City, CA, USA) according to manufacturer’s instructions. The real time amplification was repeated three times for each sample and the miR-U6B was used as endogenous control. Comparative CT method as well as ΔΔCT and 2-ΔΔCT were used to analyze the miRNA expression level. Real time PCR was performed on ABI 7500 Fast Sequence Detection System (Applied Biosystems, Lifetechnologies, USA). The expression levels of lung cancer tissues and control tissues were compared to study the relationship between miR-196a2 expression and lung cancer risk. Three groups of tissues for three types of rs11614913 SNP were analyzed to evaluate the association between rs11614913 genotypes and the expression of miR-196a2.
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5

Optimized RNA Extraction and qPCR for Pancreatic Tissues

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RNA from pancreata and other organs followed the procedure described earlier [15 (link)]. Total RNA was quantified by Nanodrop 2000 (Thermo Scientific, Zug, Switzerland) and a quality control was performed by a Bioanalyzer 2100 (Agilent, Basel Switzerland). Subsequently, 1 μg total RNA was reverse transcribed and used for real-time polymerase chain reaction (PCR) as described previously [15 (link), 30 (link)] or with a newly established method using the Precellys®24 Dual homogenizer (VWR, Dietikon, Switzerland) with MagNA Lyser Green Beads from Roche Applied Science (Basel, Switzerland). In brief, a small piece of snap frozen tissue was transferred to a tube containing beads, 650 ml of Lysis buffer (Qiagen, Hilden, Germany) was added and the tube immediately homogenized in a Precellys shaker for 30 seconds at 6000 rpm. RNA was extracted following the Qiagen RNeasy Mini Kit extraction protocol with an on column DNase digestion. Purified RNA was reverse transcribed into cDNA using qScript™ cDNA SuperMix of Quantabio (Beverly, MA, USA) according to the manufacturer’s protocol. Quantitative PCR was then performed on an ABI 7500 FAST sequence detection system (Applied Biosystems, Zug, Switzerland).
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6

Quantification of microRNA-363-3p expression

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Total RNA was extracted from serum and cells using TRIzol reagent (Invitrogen; Thermo Fisher Scientific, Inc.). cDNA synthesis was carried out using a RT kit (Takara Biotechnology Ltd.). MicroRNA-363-3p expression was quantified by using SYBR Premix Ex TaqTM (Takara) under ABI 7500 Fast Sequence Detection System (Applied Biosystems Prism; Thermo Fisher Scientific, Inc.).
Microarray analysis was performed using Illumina, HT-12 v4.0 platform (Bencos Research Solutions). Total RNA was extracted from serum and cells using TRIzol reagent (Invitrogen; Thermo Fisher Scientific, Inc.). Gene expression analysis was performed commercially using Illumina, HT-12 v4.0 platform and expression of genes was analyzed using R 3.1.2 (www.r-project.org).
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7

Cardiac mRNA Expression Analysis

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Total mRNA was isolated from the left ventricle of the heart (n = 5 per group) using QIAzol lysis reagent and Qiagen RNeasy mini kit (Qiagen) with on-column deoxyribonuclease I step (Qiagen) according to manufacturer’s protocol as previously described16 (link). 2 μg of mRNA was reverse transcribed into cDNA using High Capacity cDNA Reverse Transcription Kit (Applied Biosystems). Real-time polymerase chain reaction (RT-PCR) was detected on ABI 7500 Fast Sequence Detection System (Applied Biosystems) and analyzed by 7500 Fast System Software (Applied Biosystems). Primers and probes (Supplementary table 1) were designed with PrimerExpress 3.0 (Applied Biosystems) and synthesized by Biotez (Germany). Analysis of target mRNA expression was performed with RT-PCR using the relative standard curve method. The expression level of the target genes was normalized by the expression of the 18S housekeeping gene. Samples were run in triplicates and mean was used for further calculations. The arbitrary units reflect the ratio of the target mRNA concentration divided by the concentration of 18S of the same sample.
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8

RNA Extraction and Quantitative RT-PCR

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RNA extraction was conducted using Trizol reagent per the manufacturer’s instructions (Invitrogen, CA, USA), followed by treatment with DNase I and reverse transcription using oligo d(T) priming and Superscript III reverse transcriptase (Invitrogen). Primer sequences for real-time quantitative reverse transcription PCR (qRT-PCR) are listed in Supplementary Table S1. Quantitative RT-PCR was conducted using an ABI 7500 fast sequence detection system (Applied Biosystems, Grand Island, NY, USA), and transcript abundance was normalized to the constitutively expressed ribosomal protein S2 (Rps2), calculated using the 2−∆∆Ct formula, as described previously [23 (link)].
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9

RNA Extraction and Real-Time RT-PCR

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RNA was extracted using TRI Reagent (MRC Inc., Cincinnati, OH) according to the manufacturer’s recommendation followed by DNase digestion and column cleanup using QIAGEN mini columns. RNA isolation from cultured cells: treated cells from 12-well plates were washed twice with PBS, 1000 µl TRI Reagent was added into each well. Cells were scraped into a 1.5-ml Eppendorf tube. RNA preparation was the standard TRI Reagent protocol. Reverse transcription was carried out using an iScript cDNA synthesis kit from Bio-Rad (Hercules, CA). Real-time RT-PCR was carried out using SYBR Green and an ABI 7500 Fast sequence detection system (Applied Biosystems, Foster City, CA).
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10

Quantitative RT-PCR Analysis of NSCLC

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Total RNA was extracted from NSCLC cells and tissues using the Trizol method. RNA concentration was measured using an ultraviolet spectrophotometer (IMPLEN, Germany). Subsequently, extracted RNA was reverse transcribed into cDNA according to the instructions of the PrimeScriptTM RT MasterMix kit (Takara, Dalian, China). PCRs were performed by using the SYBR Green method in an ABI 7500 FAST sequence detection system (Applied Biosystems). The thermal cycle was as follows: 30 s at 95 °C, 3 s at 95 °C, and 30 s at 60 °C for 40 cycles. The primer sequences used in the present study are given in Table 1. The primers were synthesized by Sangon Biotech (Shanghai) Co., Ltd., (Shanghai, China).
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