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45 protocols using omniscript rt

1

Real-Time qPCR Expression Analysis

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RNA was isolated from the tissues and cell lines using RNeasy kits, and cDNA was synthesized with an Omniscript RT (Qiagen, Inc.) kit from 2 μg of the RNA. The cycling conditions were as follows: 95°C for 20 s, followed by 40 cycles of 95°C for 15 s, and 58°C for 1 min. The expression was estimated by 2−ΔΔCt method and actin was used as an internal control [13 (link),14 (link)]. The transfection of KGN with different cell constructs was carried out using Lipofectamine 2000 reagent as per the manufacturer’s guidelines.
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2

Quantitative real-time PCR for stem cell gene expression

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Equivalent numbers of EBs were collected in 100–200 μl of commercially available (Qiagen) RLT buffer at intended time points. RNAs were isolated using Qiagen RNeasy Mini Kit (Qiagen 74104) and cDNA was synthesized using Omniscript RT (Qiagen 205111). Taqman Assay reagents (Universal PCR 2X master mix; Applied Biosystems 4304437) were used for all targets. The reactions were quantified using Applied Biosystems ABI7300 PCR and ViiA7 detection systems and software. All Ct values were manually checked. cDNAs were diluted when necessary to avoid Cts lower than 18. Taqman Assays: Gsc (Mm00650681_g1), Nes (Mm00450205_m1), Pouf51 (Mm00658129_gH), Mixl1 (Mm00489085_m1), Nanog (Mm02019550_s1) Trim33 (Mm01308695_m1); all from Thermo-Fisher Scientific. Actb: Forward Primer (tgacaggatgcagaaggaga), Reverse Primer (cgctcaggaggagcaatg), Universal Probe #106 (Roche).
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3

Comprehensive Lipid Metabolism Profiling

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Infinity Cholesterol (catalog #TR13421), Infinity Triglyceride (catalog #TR22421), and TRIzolTM (catalog #15596018) reagents were purchased from Thermo Fisher Scientific (Middletown, VA, USA). Autokit Glucose (catalog #997-03001), Phospholipids C (catalog #997-01801), and HR Series NEFA-HR(2) (catalog #999-34691, 995-34791, 991-34891, and 993-35191) kits were purchased from Fujifilm Wako Chemicals USA (Richmond, VA, USA). Omniscript RT (catalog #205113) kit was purchased from Qiagen (Germantown, MD, USA) and qPCRTM core kit for SYBR Green I (catalog #10-SN10-05) was from Eurogentec (San Diego, CA, USA). 3H-cholesterol (catalog #NET139001MC), 14C-oleic acid (catalog #NEC317250UC), and 14C-triolein (catalog #NEC674250UC) were from PerkinElmer (Shelton, CT, USA). Poloxamer 407 (catalog #P1166) was purchased from Spectrum Chemical (New Brunswick, NJ, USA). Primary and secondary antibodies were purchased from either Cell Signaling (Danvers, MA, USA) or Abcam (Cambridge, MA, USA). All other chemicals and solvents were obtained from Fisher Scientific through its local distributor in the Kingdom of Saudi Arabia.
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4

Quantitative Real-Time PCR Protocol

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Total RNA was isolated with NucleoSpin® RNA II (Macherey-Nagel) and reverse transcribed using Omni-script RT (Qiagen). PCR amplification was performed as previously described (41 (link)). For qPCR cDNA samples were mixed with iQTM SYBR® Green Supermix and analyzed on iQTM5 Multicolor Real-Time PCR Detection System (Bio-Rad). Relative gene expression was calculated using iQTM5 Optical System Software. All specific primer pairs are listed in Supplementary Table S1.
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5

Interferon Gene Expression Analysis Protocol

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RNA was extracted from cells using the RNeasy method (RNeasy Mini Kit; Qiagen) following the manufacturer's instructions, including DNaseI digestion (Dnase (Rnase free Dnase); Qiagen). cDNA was synthesized using Omniscript RT and components as directed by the manufacturer (Qiagen). Sequences, concentrations of primers and probes for the detection of human IFN-α.1 (detecting IFN-α subtypes 1, 6 and 13), -α.2 [2 (link),4 (link),5 ,8 (link),10 (link),14 (link),17 (link) and 21 (link)], IFNB, IL28A/B, IL29, 18S and conditions of RT-qPCR reaction were used as previously described [28] (link). Relative quantification of RT-qPCR was used to detect changes in expression of the interferon genes relative to a reference gene, the housekeeping human 18S gene. Quantitative PCR results for mRNA expression are presented as ΔCt values, calculated by the formula: ratio (reference/target)=2Ct(reference)-Ct(target). The number of copies for viral RNA quantification was calculated using a standard curve generated by amplification of plasmid DNA.
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6

Quantitative Real-Time PCR for Gene Expression

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The total RNA was extracted from the PTC cells with the help of TRIzol reagent (Thermo Fisher Scientific). To reverse transcribe the cDNA, the Omniscript RT (Qiagen NV, Venlo, the Netherlands) was employed using 1 µg of the extracted RNA. The cDNA was then used as a template for quantitative real-time PCR (qRT-PCR) with the help of Taq PCR Master Mix Kit (Qiagen NV) according to the manufacturer’s instructions. The primer sequences used in the present study were as follows: RECK, forward 5′-AGCAACCGAGCCCGTATGT-3′ and reverse 5′-CCGAGTAGGCAGCACACACA-3′; U6, forward 5′-TGG GGTTATACATTGTGAGAGGA-3′ and reverse 5′-GTGTG CTACGGAGTTCAGAGGTT-3′; and β-actin, forward 5′-ATGGATGATGATATCGCCGCGCTC-3′ and reverse 5′-TTTCTCCATGTCGTCCCAGTTGG-3′. β-Actin was used as the internal control. The relative expression levels of each gene were detected and normalized using the 2−ΔΔCt method relative to U6 or β-actin. Experiments were performed in triplicate.
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7

PBMC Isolation and RNA Extraction

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PBMCs were isolated from EDTA blood by density gradient centrifugation on Lymphoprep™ by Axis-Shield (Sentinel Diagnostic, Milan, Italy). Total RNA was extracted and purified using the Omega Bio-Tek E.Z.N.A.™ total RNA kit (VWR International, Milan, Italy) according to the manufacturer's instructions. After DNA digestion with DNase I enzyme (Qiagen, Milan, Italy), complementary DNA was synthesized from 1 μg of total RNA using Omniscript RT (Qiagen, Milan, Italy) and random hexamers.
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8

Quantification of Gene Expression in H9c2 Cells

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Total RNA was extracted from H9c2 cells using Trizol reagent (Invitrogen) followed by DNase digestion for 10 min at room temperature with RNase-Free DNAse Set (Qiagen), and cleaned up with RNeasy Mini Kit (Qiagen). The quality of the RNA was determined by electrophoresis through agarose gels; only RNA samples with 28S:18S, rRNA ratio ≥ 2were used. Oligo-dT primer was used to target mRNAs present in the total RNA samples for conversion into cDNAs by reverse transcriptase (RT). Cleaned-up total RNA (2 μg) was reverse transcribed in a final volume of 20 μL containing 1x RT buffer, 0.5 mM dNTP Mix, 10 units of RNasin RNase inhibitor (Promega), 4 units of Omniscript RT (Qiagen), and 1 μM oligo-dT primer. Samples were incubated at 37°C for 60 min, followed by RT inactivation at 95°C for 5 min. Real-time PCR and gene-specific primers were used for quantification of TGF-β, PGC1-α, Nrf1, and YAP-responsive genes and FOXO3 responsive genes using Fast SYBR™ Green Master Mix (ThermoFisher, catalog number 4385614). The specificity of the reaction was verified by melt curve analysis. The relative quantification in gene expression was determined using the 2–ΔΔCt method (59 (link)). Using this method, we obtained the fold changes in gene expression normalized to internal control genes (β-actin, and/or GAPDH). The following primers were used for amplification
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9

Quantitative Gene Expression Analysis

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Total RNA from tissues and cells were isolated using TriZol. The first-strand complementary DNA was then synthesized using Omniscript RT (Qiagen) kit, and then used for quantitative RT–PCR using SYBR Green to quantify changes in mRNA. The data were analysed using the ΔΔCT method and presented as arbitrary units16 (link)17 (link).
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10

RNA Extraction and Quantification Protocol

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Right ventricles were crushed in TRIzol for RNA extraction as previously described 25. Cell RNA extractions were performed using the TaKaRa CellAmp Direct RNA kit (Clontech Saint‐Germain‐en‐Laye, France) as per the manufacturer's protocol. For miR‐322‐5p measurements, RNA was reverse‐transcribed (RT) using miR‐322‐5p and U6 Applied Biosciences TaqMan primers suspended in 1x TE buffer as per the manufacturer's instructions. cDNA was used for qPCR with TaqMan fluorescent probes for miR‐322‐5p and U6 according to the manufacturer's instructions. mRNA was measured via Omniscript RT (Qiagen, Manchester, UK) with random primers (Promega, Madison, WI, USA) as per the manufacturer's protocol. cDNA was diluted 1/10 with deionised water and used in qPCRs with QuantiFast SYBR Green (Qiagen) and specific primers (Sigma, Poole, Dorset, UK) for targets of interest as previously described 26.
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