The largest database of trusted experimental protocols

7 protocols using ssofast sybr green supermix

1

Gene Expression Analysis by qPCR

Check if the same lab product or an alternative is used in the 5 most similar protocols
Total RNA was isolated using RNeasy Isolation Kit according to the manufacturer's instructions (Qiagen). cDNA was synthesized with the Superscript III First-Strand Synthesis system (Invitrogen), and real-time PCR was performed on a Bio-Rad iCycler with SSOFast SYBR Green Supermix (Bio-Rad) and primer pairs specific for cDNA (5′ to 3′) were as follows: IL17A Forward: TTTAACTCCCTTGGCGCAAAA, IL17A Reverse: CTTTCCCTCCGCATTGACAC; IL17F Forward: TGCTACTGTTGATGTTGGGAC, IL17F Reverse: AATGCCCTGGTTTTGGTTGAA; CCR6 Forward: CCTGGGCAACATTATGGTGGT, CCR6 Reverse: CAGAACGGTAGGGTGAGGACA; CCL20 Forward: GCCTCTCGTACATACAGACGC, CCL20 Reverse: CCAGTTCTGCTTTGGATCAGC. Quantification of relative mRNA expression was determined by the comparative CT (critical threshold) method where the amount of target mRNA, normalized to endogenous β-actin expression, is determined by the formula 2-ΔCT and was represented as 2−ΔCt, where ΔCt = CtIL2 – CtActin. In some experiments, normalized Ct values were presented as an induction relative to expression in control samples.
+ Open protocol
+ Expand
2

Quantitative RT-PCR Analysis of Arabidopsis RNA

Check if the same lab product or an alternative is used in the 5 most similar protocols
Total RNA was extracted from inflorescences using PureZol RNA Isolation Reagent (Bio-Rad) following the manufacturer’s instructions. DNA was removed by DNase (Thermo Scientific) treatment. Isolated RNA samples were reverse transcribed using RevertAid First Strand cDNA Synthesis kit (Thermo Scientific) and oligo(dT)18 primers to initiate the reactions. Complementary DNA (cDNA) was amplified using the SSoFAST SYBR Green Supermix (Bio-Rad) in an iQ5 Real-Time RT-PCR (Bio-Rad) detection system using specific primers listed in Supplementary Table 1. Primers for the reference genes ACTINA8 ACT8 (At1g49240) and ARABIDOPSIS THALIANA RELATED TO UBIQUITIN 1 RUB1 (At1g31340) were used. Three technical replicates were performed for each situation. After 3 min at 95°C, a 10s denaturation step at 95°C was followed, and 45 cycles of 95°C at 10s and 60°C at 30s were performed. After amplification, the dissociation curve was acquired to verify the specificity of the amplification by heating the samples from 60 to 95°C. At the end of the PCR cycles, data were analyzed using the CFX Maestro™ Software (Bio-Rad) program.
+ Open protocol
+ Expand
3

Quantitative RT-PCR Analysis of Transcription Factors

Check if the same lab product or an alternative is used in the 5 most similar protocols
RNA was isolated using RNeasy mini kit (Qiagen). Digested with DNaseI (Sigma-Aldrich) for 15 min at RT to remove DNA contamination, and subsequently, DNaseI was inactivated by heating at 70 °C for 10 min. cDNA was synthesized using Qscript supermix (Quanta Biosciences). Real-time PCR was performed using SSO fast SYBR green supermix (Bio-Rad) in a 7500 real-time PCR system (Applied Biosystems) using 7500 software v2.0.1. Melting curve analysis was performed to ensure the amplification of a single product. Primers used were the following: TCF-1-F-5′-AGGCCAAGAAGCCAACCATCAAGA and TCF-1-R-5′-ACTCTGCAATGACCTTGGCTCTCA; TCF-3-F-5′-TGCAGTGAGCGTGAAATCACCAGT and TCF-3-R-5′-AATGGCTGCACTTTCCTTCAGGGT; TCF-4-F-5′-TCGGCAGAGAGGGATTTAGCTGATGT and TCF-4-R-5′-CTTTCCCGGGATTTGTCTCGGAAACT; LEF1-F-5′-AAGCATCCAGATGGAGGCCTCTACAA and LEF1-R-5′-TGATGTTCTCGGGATGGGTGGAGAAA; β-catenin-F-5′-TCTTGCCCTTTGTCCCGCAAATCA and β-catenin-R-5′-TCCACAAATTGCTGCGTCCCA; EAAT2-F-5′-CCAAGCTTGGATCACTGCCCTGG and EAAT2-R-5′-CCAGCCCCAAAAGAGTCACCCACAA; GS-F-5′-TTGAGAAACTAAGCAAGCGGCACC and GS-R-5′-ATCCAGTTAGACGTCGGGCATTGT; and GAPDH-F-5′-CTTCAACGACCACTTTGT and GAPDH-R-5′-TGGTCCAGGGGTCTTACT. Fold change in messenger RNA (mRNA) expression was calculated by relative quantification using the comparative CT method with GAPDH as the endogenous control.
+ Open protocol
+ Expand
4

Quantitative Analysis of HPV Gene Expression

Check if the same lab product or an alternative is used in the 5 most similar protocols
cDNA was synthesized from 1 μg of RNA using the iScript cDNA Synthesis Kit (Catalog #170-8890; Bio-Rad, Hercules, CA) according to the manufacturer’s protocol. The synthesized cDNA was used as a template to determine the HPV E6 and E7 gene expression levels for HPV types 16, 18, 33, 45, and 68. To determine relative HPV viral gene expression levels, genomic DNA was isolated, and HPV E6, E7, and GAPDH primers were used for real-time, quantitative PCR (Supplementary Table 8). Each 20-μL RT-PCR reaction contained 1× SsoFast SYBR Green SuperMix (Bio-Rad), a 100-nM concentration of each primer, and 25 ng of DNA. Thermocycling conditions were 98°C for 2 minutes for 1 cycle, 98°C for 30 seconds, and 60°C for 5 seconds for 40 cycles.
+ Open protocol
+ Expand
5

RNA Isolation and RNAseq Analysis

Check if the same lab product or an alternative is used in the 5 most similar protocols
RNA was isolated from muscles, and gene expression and RNA sequencing (RNAseq) was performed as described 20 (link). Samples were homogenized in QIAzol (Qiagen, Valencia, CA) and RNA was isolated using 5PRIME Phase Lock Gel tubes (Quantabio, Beverly, MA), an RNeasy Mini kit (Qiagen), and DNase I (Qiagen). RNA concentration and quality were assessed using a NanoDrop One (Thermo Fisher Scientific) and a BioAnalyzer 2100 (Agilent, Santa Clara, CA). All samples had RIN values > 8.1.
A total of 250ng of RNA was delivered to the Weill Cornell Epigenomics Core for processing and sequencing. cDNA pools were created for each sample, and then subsequently tagged with a barcoded oligo adapter. Sequencing occurred in an Illumina HiSeq 2500 system (Illumina, San Diego, CA) with 50bp single end reads. Data quality was checked using FastQC, and aligned to the reference genome (mm10, UCSC, Santa Cruz, CA). Differential expression was calculated using edgeR 29 (link). Complete RNAseq data is available through NIH GEO (ascension number GSE130447).
For quantitative PCR (qPCR), RNA was reverse transcribed into cDNA using iScript Supermix (Bio-Rad). cDNA was amplified in a CFX96 real-time thermal cycler (Bio-Rad) using SsoFast SYBR Green Supermix (Bio-Rad). Target gene expression was normalized to the housekeeping gene casein kinase 2α1 (Csnk2a1) using the 2−ΔCt method.
+ Open protocol
+ Expand
6

Quantitative RT-PCR for Gene Expression

Check if the same lab product or an alternative is used in the 5 most similar protocols
For RNA: The RPE/choroid complex or neuroretina was dissected out and placed in Trizol reagent (Invitrogen, 15596026) and RNA was extracted according to the manufacturer's protocol. To obtain cDNA templates, iScript reverse transcription mix was used (Bio-Rad; Hercules, CA). For Real-Time PCR: Primers were designed as described [22 (link)]. Real-time PCR was performed using Ssofast SYBR Green Supermix (Bio-Rad; Hercules, CA) and the MyiQ Single-Color Real-Time PCR system (Bio-Rad; Hercules, CA) using the manufacturer's instructions and as described [22 (link)]. Primer sequences are listed in Supplementary Table 1. Primers for PKM1 and PKM2 were obtained from Casson et al. [23 (link)]. mRNA expression was normalized to RPL19 and then to the WT control.
+ Open protocol
+ Expand
7

Quantitative RT-PCR of Zinc-Responsive Genes in P. aeruginosa

Check if the same lab product or an alternative is used in the 5 most similar protocols
The quantitative real-time RT-PCR with the rpsl gene as the reference was performed to monitor the expression changes of czcS, czcR, czcC and oprD genes when P. aeruginosa is stimulated by the Zn(II) at a micromolar level. The total RNA was extracted by traditional phenol-chloroform method and reverse transcribed by iScript cDNA Synthesis Kit (Bio-Rad). The cDNA samples were diluted for different folds and used as the templates in the PCR experiments. The real-time RT-PCR was performed on the Bio-Rad CFX96 equipment using the Ssofast SYBR Green Supermix (Bio-Rad). The experiments were performed at least three independent times with average results shown. The primer sequences used for real-time RT-PCR are designed using the Primer3 program and listed in S3 Table.
+ Open protocol
+ Expand

About PubCompare

Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.

We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.

However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.

Ready to get started?

Sign up for free.
Registration takes 20 seconds.
Available from any computer
No download required

Sign up now

Revolutionizing how scientists
search and build protocols!