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10 protocols using iq5 optical system software v2

1

Quantitative Gene Expression Analysis

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RNA was extracted from 100 mg leaf disk using Triazol reagent (Sigma-Aldrich) according to the manufacturer’s instructions. RNA (5 ug) was treated with RNase-free DNase1 (Ambion). RNA (2 ug) was used to make random-primed cDNA except that the MuMLV reverse transcriptase was purchased from Fisher. Quantitative real-time PCR of the cDNA was performed using EvaGreen-fluorescence based procedure with reagents purchased from Applied Biological Materials (Canada). Relative and normalised fold expression values were calculated using the iQ5 Optical System Software v2.1 (Bio-Rad) normalised with respect to relative cDNA levels for CYCLOPHILIN (Niben101Scf01694Ctg023) and ZIP9 (Niben101Scf03839Ctg048). The primers used in this study for quantitative RT-PCR are given in Supplementary Table 1.
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2

Quantitative Real-Time PCR Analysis

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RNAs were extracted as above, and reversed transcribed to cDNA by the GoScript Reverse Transcription System (Promega, A5001) following the manufacturer's instructions. The qRT-PCR reaction was performed by MyiQ2 (BIO-RAD) and analyzed by the iQ5 Optical System Software V2.1 (BIO-RAD) and SYBR Green chemistry (Vazyme). All the PCR results were presented relative to the mean of input data, negative control pie-1 mRNA (39 (link)) and mean of N2 worms (Supplementary data 6 and 7). Primers for qRT-PCR analyses are shown in Supplementary Table S9. The data and figures were analyzed and visualized by Origin 2019 (OriginLab).
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3

Quantitative Real-Time PCR Analysis

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For qRT-PCR, 5 μg of RNase-free DNase I-treated RNA was processed with M-MLV reverse transcriptase (Takara Bio Inc., Japan) according to the manufacturer’s instructions. Relevant PCR primers directed against a selection of differentially transcribed sequences identified by iTRAQ (Additional file 1) were designed using Beacon Designer 8.0 software (Premier Biosoft International, Palo Alto, CA, USA). A fragment of the gene encoding 18S rRNA was used as a reference. PCR was performed with a Bio-Rad iQ5 instrument (Bio-Rad, Hercules, CA, USA), using SYBR Green to detect transcript abundance. Each 25-μL reaction contained 0.5 μM of each primer and approximately 0.5 U of enzymes, cDNA and SYBR Green. Negative control reactions contained no cDNA. Five-fold dilutions of the cDNA templates were tested under conditions identical to those used for the samples being tested. The PCR regime included an initial denaturing step (95 °C/10 s), followed by 40 cycles at 95 °C/5 s, 60 °C/10 s, and 72 °C/15 s and a final stage at 55 °C to 95 °C to determine dissociation curves of the amplified products. All reactions were replicated at least three times. The data were analysed using Bio-Rad iQ5 Optical System Software v2.1. The relative transcript level of each gene was calculated using the 2-△△CT method, and the data were normalized based on the 18S rRNA CT values [43 (link)].
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4

Quantitative RT-PCR Analysis of Gene Expression

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Total RNA was isolated from cells with TRIzol reagent (Invitrogen) according to the manufacturer's instructions. Total RNA was reverse-transcribed using the iScript Select cDNA Synthesis Kit (Bio-Rad, Hercules, CA) and realtime quantitative PCR were run in triplicate for each sample on a Bio-Rad My Cycler iQ5 (Bio-Rad). Primer sequences were obtained from Stabvida (Costa da Caparica, Portugal) and thoroughly tested. The resulting RT product was expanded using the Syber Green Supermix (Bio-Rad). The results were then normalized to the expression of a housekeeping gene Srp72. After amplification, a threshold was set for each gene and cycle threshold-values (Ct-values) were calculated for all samples. Gene expression changes were analysed using the built-in iQ5 Optical system software v2.1 (Bio-Rad). The complete list of primers used is given in Table 1.
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5

RNA Extraction and Gene Expression Analysis

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Total RNA extraction from MDA-MB-231 was carried out using the RNeasy Mini Kit (Qiagen). For cDNA synthesis, total RNA (1 μg) was transcribed using random hexamers (Invitrogen, Carlsbad, CA), and SuperScript III reverse transcriptase (Invitrogen) following the manufacturer’s protocol. For quantification of OXPHOS-related genes, the cDNA amplication program included a denature at 95°C for 3 min, followed by 40 cycles of 95°C for 10 s; 58°C for 30 s. For MtDNA detection, total cellular DNA was isolated with DNAeasy Blood and Tissue Kit (Qiagen). Mitochondrial DNA content was determined by qPCR by using comparing the mitochondrially encoded Cox2 gene to an intron of the nuclear-encoded β-globin (HBB) gene. All qPCR was performed using an iQ5 iCycler (Bio-Rad) according to the manufacturer’s instructions. Data were analyzed using Bio-Rad iQ5 Optical System Software v2.0. All products yielded a single band with the predicted size. All primers are listed in Additional file 1: Table S1 and all products yielded a single band with the predicted size.
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6

Quantitative Analysis of WNT Gene Expression

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For complementary DNA (cDNA) synthesis, total RNA (1 mg) was transcribed using random hexamers (Life Technologies) and SuperScript III reverse transcriptase (Life Technologies) following the manufacturer's protocol. For DNA amplification, cDNA was denatured at 94°C for 30 s, and primers were annealed at 55–62°C for 30 s. DNA extension was performed at 72°C for 30 s for 24–30 cycles. Real-time RT–PCR analyses of WNT2B, WNT3, WNT5A, WNT5B, WNT6, WNT7A, WNT9A, WNT10A and WNT10B were performed using an iQ5 iCycler (Bio-Rad, Hercules, CA) according to the manufacturer's instructions. The amplification conditions consisted of an initial incubation at 95°C for 10 min, followed by 40 cycles of 95°C for 10 s and 59°C for 30 s. The data were analyzed using Bio-Rad iQ5 Optical System Software v2.0. All products yielded a single band of the predicted size.
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7

Quantitative RT-PCR Analysis of Gene Expression

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Here, 5 μg of RNA was treated with DNase I and reverse transcribed using the RevertAid H Minus First Strand cDNA Synthesis Kit (Thermo Fisher Scientific, Waltham, USA) according to the manufacturer’s protocol with a combination of oligo(dT) and random hexamer primers. Three biological replicates were pooled prior to RNA extraction. PCR reactions were performed in triplicate on a Bio-Rad (Hercules, CA) iCycler IQ using IQ SYBR Green Supermix (Bio-Rad, Hercules, CA, United States), standard MgCl2 concentration (3 mM), and a final primer concentration of 100 nM in a total volume of 25 μl. Primer sequences with the corresponding parameters are provided in Supplementary Table 3. The PCR protocol comprised an initial denaturation step (2 min at 95°C) followed by 40 cycles of denaturation (5 s at 95°C), annealing (20 s, for Tm, see Supplementary Table 3) and extension (65°C for 10 s). qPCR efficiency was determined using triplicate reactions from a dilution series (1, 0.1, 10–2, and 10–3) of cDNA. The given slopes in the IQ5 Optical system Software v2.0 (Bio-Rad, Hercules, CA, United States) were used to calculate the amplification efficiency. Expression ratios and standard errors were determined using Pfaffl test model in REST (Pfaffl et al., 2002 ) with sar1 as reference gene (Brunner et al., 2008 (link)).
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8

Phylogenetic Analysis and qRT-PCR of JHAMT Isoforms

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We used the JHAMT protein sequences from the following species: A. aegypti melanogaster (AAF46666) and S. gregaria (HQ634704). Sequences were aligned using the iterative refinement method G-INS-i from the program MAFFT v. 7 (Katoh & Standley, 2016) . The alignment was analyzed using the RAxML-HPC BlackBox tool of the CIPRES Science Gateway v. 3.1 (Miller et al., 2010) . The data sets were bootstrapped for 100 replicates.
RNA extraction, cDNA synthesis and real-time PCR analyses cDNAs were synthetized using as previously described (Abrisqueta et al., 2017) . The absence of genomic contamination was confirmed using a control without reverse transcription. Gene expression was analyzed by quantitative real-time PCR using iQ SYBR Green supermix in an iQ cycler and iQ single color detection system and the iQ5 optical system software v. 2.0 (Bio-Rad Laboratories, Hercules, CA, USA), as previously described (Maestro et al., 2010) . Primers used to amplify total BgJHAMT as well as the different 3'-UTR isoforms can be found in Table S1. Primers used to amplify vitellogenin (BgVg) and BgActin 5C (used as a reference) have been already reported (Süren-Castillo et al., 2012) . The primers efficiencies were validated by constructing serial cDNA dilutions standard curves. Results were expressed as copies of a specific mRNA per copies of BgActin 5C.
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9

Quantitative Analysis of Corpora Allata and Fat Body Gene Expression

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The corpora allata and fat body mRNA levels of the different studied genes were analysed using quantitative real-time PCR. cDNAs were synthesized from total RNA as previously described (Abrisqueta et al., 2014; Maestro et al., 2009) . In the case of fat bodies, 500 ng of total RNA was used, whereas for corpora allata, the whole RNA from one pair of glands was used. The absence of genomic contamination was confirmed using a control without reverse transcription. The cDNA levels were quantified using iQ SYBR Green supermix in an iQ cycler and iQ single colour detection system and the iQ5 optical system software v. 2.0 (Bio-Rad Laboratories, Hercules, California), as previously described (Maestro et al., 2010) . Primer sequences to amplify BgS6K can be found in Table S1. Primers used to amplify HMG-CoA synthase-1 and -2, HMG-CoA reductase, vitellogenin (BgVg) and BgActin 5C (used as a reference) have been already reported (Maestro et al., 2010; Suren-Castillo et al., 2012) . The total reaction volume was 20 µL. All reactions were run in duplicate or triplicate. Results were expressed as copies of a specific mRNA per copies of BgActin 5C.
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10

Quantitative Gene Expression Analysis

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The expression levels of the different genes studied were analyzed using quantitative real-time PCR (qRT-PCR) in cDNA prepared from different tissues. cDNA was synthesized from total RNA as described above. The absence of genomic contamination was confirmed using a control without reverse transcription. cDNA amplifications of OKA, OKB, Vg, 3-hydroxy-3-methylglutaryl coenzyme A synthase 1 (HMG-CoA synthase-1), juvenile hormone acid methyltransferase (JHAMT) and actin 5C were performed in duplicate or triplicate, in a 20 ll final volume (primers detailed in Supplementary Table 1). cDNA levels were quantified using iQ SYBR Green supermix (Bio-Rad) in an iQ cycler and iQ single colour detection system (Bio-Rad). The schedule used for the amplifying reaction was as follows: (i) 95 °C for 3 min, (ii) 95 °C for 10 s; (iii) 57 °C for 1 min; (iv) steps (i) and (ii) were repeated for 50 cycles. Real-time data was collected through the iQ5 optical system software v.2.0 (BioRad). For quantification of soluble proteins, ovaries were dissected and placed at À80 °C until their use. Total soluble proteins were extracted by ultrasonication and centrifugation in NaCl 0.4 M solution and quantified according to Bradford (Bradford, 1976) .
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