All samples were collected from untreated HCV genotype 1 infected patients. The zinc study cohort consists of the pre-treatment serum samples from 100 patients taken at the first clinical visit. Parallel liver function and clinical blood tests were performed by the Institute for Clinical Pathology and Medical Research (ICPMR) at Westmead Hospital, Sydney. The microarray sample cohort consists of 22 patients liver biopsies20 (link), 17 of which belong to the zinc study cohort. Briefly, liver biopsy RNA was isolated using the Qiagen RNeasy kit and mRNA was hybridized to Illumina Human HT-12 V3 arrays according to the manufacturers instructions. Signal intensity was measured using Beadstudio version 3 and cubic spline normalization was applied. Microarray data is available in the Dryad repository under doi:10.5061/dryad.n0s75 . Ethics approval was obtained from the Sydney West Area Health Service and University of Sydney. All subjects have given written formal consent (HREC2002/12/4.9(1564)). All subjects were genotyped for the IFN-λ SNP rs12979860 using Taqman genotyping probes (ThermoFisher)20 (link).
Taqman genotyping probes
Manufactured by Thermo Fisher Scientific
Sourced in United States
TaqMan genotyping probes are a type of fluorescent probe used for real-time PCR analysis. They are designed to detect and quantify specific DNA sequences during the amplification process. The probes consist of a fluorescent reporter dye and a quencher dye, which are separated when the probe binds to the target DNA, allowing the reporter dye to emit a fluorescent signal.
Automatically generated - may contain errors
Lab products found in correlation
Lc480, by Roche (3 mentions)
Lightcycler 480 probes master mix, by Roche (2 mentions)
Rneasy kit, by Illumina (1 mentions)
Lightcycler 480, by Roche (1 mentions)
Abi prism 3730xl automated dna sequencer, by Thermo Fisher Scientific (1 mentions)
Rotor gene q, by Qiagen (1 mentions)
Qiaamp dna blood mini kit, by Qiagen (1 mentions)
Taqman universal pcr master mix, by Thermo Fisher Scientific (1 mentions)
6 protocols using taqman genotyping probes
1
Zinc Status in Chronic Hepatitis C: Transcriptional Profile
2
VEGFA Genotyping in CDCS Cohort
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
DNA samples were obtained for 2067 CDCS cohort patients. Extraction of genomic DNA for genotyping was performed as described previously [22 (link),24 (link)]. DNA samples were genotyped for the rs699947 (C-2578A, assay ID C_8311602_10), rs2010963 (C405G, assay ID C_8311614_10) and rs3025039 (C936T, assay ID C_16198794_10) polymorphisms in VEGFA using 5 μL reaction volumes in 384-well plates with allele-specific TaqMan genotyping probes (ThermoFisher Scientific). Genotyping reactions including 1x Roche LightCycler 480 Probes Master mix and 100ng of genomic DNA were performed in a Roche LC480 (Roche Diagnostics Ltd., Rotkreuz, Switzerland) as described elsewhere [24 (link)]. Linkage disequilibrium data as determined for the 3 SNPs is shown in S1 Table . As quality control a random selection of 10% of samples were re-genotyped with 100% concordance with the original genotypes.
3
Genotyping of Huntington's Disease Markers
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Selection of the majority of the markers used in this study was based upon previous work from our lab that showed that they were overrepresented on HD chromosomes. [Lee et al., 2012 ] Genotyping of nine SNPs (rs6814736, rs7667745, rs1751848, rs762847, rs7658462, rs3129317, rs1730768, rs12641989, and rs16844364 ‐ Fig. 1 ) flanking the CAG repeat was performed by real‐time polymerase chain reaction (PCR), using the commercially available Taqman Genotyping probes (Applied Biosystems, Foster City, CA), carried out on the LightCycler® 480 (Roche Diagnostics, Mannheim, Germany), following manufacturer's instructions. Repeat sizes of the HTT CAG repeat, CCG repeat and D4S127 and genotyping of the delta2642 polymorphism were determined using previously established, but slightly modified PCR amplification assays with fluorescently labelled primers. [Taylor et al., 1992 ; Rubinsztein et al., 1993 ; Warner et al., 1993 ; Ambrose et al., 1994 ] The fragments' size was then determined using the ABI PRISM 3730xl automated DNA Sequencer (Applied Biosystems, Foster City, CA) and GeneMapper version 3.7 software. For each marker, a set of sequenced samples was used as standards.
4
Genotyping VEGFR-2 and VEGFR-1 Polymorphisms
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Extraction of genomic DNA for genotyping was performed as described previously [23 (link)]. DNA samples were genotyped for the rs2071559 (T-604C), rs2305948 (G1192A), rs1870377 (T1719A) polymorphisms in the VEGFR-2 receptor gene (encoding KDR) and rs748252 (C8764T) and rs9513070 (A189427G) in the VEGFR-1 receptor gene (encoding Flt-1). The SNPs from VEGFR-1 were chosen with reference to dbSNP and International HapMap Project data, as at the time of initiating this study there were no prior reports of genetic association studies of polymorphisms in VEGFR-1 and CVD. Genotyping was performed by real-time PCR, using allele-specific TaqMan genotyping probes (Applied Biosystems) in 5 μL reaction volumes in 384-well plates, including 1× Roche LightCycler 480 Probes Master mix and 100 ng of genomic DNA in a Roche LC480 (Roche Diagnostics, Auckland).
5
Genomic DNA Extraction for Genotyping
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Extraction of genomic DNA for genotyping was performed as described previously [5] (link). DNA samples were genotyped for the rs6922269 polymorphism in 10 µL reaction volumes using allele-specific TaqMan genotyping probes (Applied Biosystems, USA), including 1× Thermo qPCR ROX Mix (Thermo, UK) and 100 ng of genomic DNA in a Roche LC480 (Roche Diagnostics, Auckland).
6
Genotyping of ADRB1 polymorphisms
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Venous blood was obtained from each subject into 5-ml EDTA tube, genomic DNA was extracted from leukocytes with automated QIAcube device using QIAamp DNA Blood Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer's guidelines. Polymorphisms were selected from candidate gene (ADRB1): (rs1801252 and rs1801253). The selected polymorphisms were genotyped by TaqMan allelic discrimination method using TaqMan genotyping probes (C_8898508_10, C_8898494_10, respectively), (Applied Biosystems, Thermo Fisher Scientific, MA, USA) and carried out by using real-time polymerase chain reaction with Rotor gene Q (Qiagen, Hilden, Germany) utilizing TaqMan Universal PCR Master Mix (Applied Biosystems®) in accordance with the manufacturer's instructions. Importantly, both the subjects and investigator were blinded to the genotypic results throughout the study period.
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
Revolutionizing how scientists
search and build protocols!