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Rt2 profiler pcr array plate

Manufactured by Qiagen
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The RT2 Profiler PCR array plate is a laboratory equipment designed for real-time PCR (Polymerase Chain Reaction) analysis. It is used to study the expression of a focused panel of genes related to a specific biological pathway or disease state.

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Lab products found in correlation

Rt2 first strand kit, by Qiagen (7 mentions) Rneasy mini kit, by Qiagen (4 mentions) Rt2 sybr green rox qpcr mastermix, by Qiagen (3 mentions) Steponeplus real time pcr system, by Thermo Fisher Scientific (2 mentions) Trizol reagent, by Thermo Fisher Scientific (2 mentions) Abi 7900 thermal cycler, by Thermo Fisher Scientific (1 mentions) 7900ht cycler, by Thermo Fisher Scientific (1 mentions) Nanodrop nd 1000, by Thermo Fisher Scientific (1 mentions) Rt2 sybr green pcr master mix, by Qiagen (1 mentions) Random primer, by Promega (1 mentions) Bioscript reverse transcriptase, by Meridian Bioscience (1 mentions) Takyon sybr mastermix, by Eurogentec (1 mentions) Rnase free water, by Qiagen (1 mentions) Cfx connect, by Bio-Rad (1 mentions) Cfx manager software, by Bio-Rad (1 mentions) Rt2 first strand synthesis kit, by Qiagen (1 mentions) Superscript 3 reverse transcriptase, by Thermo Fisher Scientific (1 mentions) Rneasy plus mini kit, by Qiagen (1 mentions) Cfx connect real time pcr detection system, by Bio-Rad (1 mentions) 7900ht real time pcr system, by Thermo Fisher Scientific (1 mentions)

Close spelling variants of this product

Custom RT2 Profiler PCR array plates RT2 Profiler PCR Array Mouse Notch Signaling Pathway plates RT2 Profiler™ PCR Array Mouse inflammatory cytokines and receptors plates RT2 Profiler 96-well PCR array plates

12 protocols using rt2 profiler pcr array plate

1

RNA-seq Gene Expression Profiling

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One ug of total RNA was reverse-transcribed into cDNA using RT2 First Strand Kit (Qiagen, Valencia, CA, USA). Custom RT2 Profiler PCR array plates including controls for human genomic DNA contamination, reverse transcription and PCR efficacy (SABiosciences, Qiagen) were used for RQ-PCR reactions performed using RT2 SYBR Green ROX qPCR Mastermix (SABiosciences) on an ABI 7900 thermal cycler (Applied Biosystems, Foster City, CA, USA) as described previously47 .
Goswami M., McGowan K.S., Lu K., Jain N., Candia J., Hensel N.F., Tang J., Calvo K.R., Battiwalla M., Barrett A.J, & Hourigan C.S. (2015). A multigene array for measurable residual disease detection in AML patients undergoing SCT. Bone Marrow Transplantation, 50(5), 642-651.
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2

Transcriptional Profiling of Steroidogenic Pathways

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Postmortem brain tissue was obtained from the eight old DHEA-supplemented animals, as described above. Total RNA was extracted from the hippocampi (HPC) and dorsolateral prefrontal cortices (PFC) using the RNeasy Mini Kit (Qiagen, Valencia, CA, USA), and converted to cDNA using the RT2 First Strand Kit (SABiosciences, Qiagen, Valencia, CA, USA). The samples were then run on custom RT2 Profiler PCR Array plates (SABiosciences) in accordance with the kit instructions. Genes selected for inclusion on this plate were chosen for their involvement in either steroidogenesis (i.e., steroidogenic enzymes or transport proteins such as steroidogenic acute regulatory protein [StAR]) or steroid responses (i.e., steroid receptors and intracellular signaling proteins involved in the estrogen response). All genes were normalized against the arithmetic mean expression value of the three housekeeping genes, ALG9, GAPDH, and RPL13A.
Sorwell K.G., Renner L., Weiss A.R., Neuringer M., Kohama S.G, & Urbanski H.F. (2016). Cognition in aged rhesus monkeys: effect of DHEA and correlation with steroidogenic gene expression. Genes, brain, and behavior, 16(3), 361-368.
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3

Transcriptional Response of Cells to Borrelia Infection

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MO3.13 cells seeded in T-75 flasks were treated with either medium or B. burgdorferi (10:1 MOI) for 6 h, after which RNA was extracted using RNeasy® mini kit (Qiagen, Germantown, MD) according to the manufacturer’s instructions. NanoDrop® ND-1000 (NanoDrop Technologies Inc., Wilmington, DE) was used to quantify RNA concentration, and 1 μg of RNA was used for cDNA synthesis (RT2 First strand kit), which was aliquoted on RT2 Profiler PCR array plates (human TLR signaling pathway) using RT2 SYBR® Green ROX™ qPCR mastermix (Qiagen, Germantown, MD). The real time PCR reactions were run on Applied Biosystems 7900HT cycler and data captured using SDS 2.4 software. All protocols were carried out according to the manufacturer’s handbook. The resulting raw data were analyzed on SABiosciences web-based software (www.SABiosciences.com/pcrarraydataanalysis.php) to determine the fold change in gene expression in cells exposed to B. burgdorferi over medium control. Fold changes (upregulation) over 1.2 fold were considered for further review. Ct values > 34 were considered as too low an expression and not included for analysis.
Parthasarathy G, & Philipp M.T. (2018). Intracellular TLR7 is activated in human oligodendrocytes in response to Borrelia burgdorferi exposure. Neuroscience letters, 671, 38-42.
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4

Quantitative PCR analysis of EMT and TGF-β/BMP pathways

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RNA (input of total RNA: 1.0 µg per reaction) was reverse transcribed using the RT2 First-Strand kit (Qiagen). Subsequently, profiler array-based quantitative PCR analysis was performed, following the instructions of the supplier, using the RT2 SYBR Green PCR Mastermix (Qiagen) and primer pre-coated RT2 Profiler PCR array plates (Qiagen) encompassing 84 pathway-focused genes per plate. Two different human-specific profiler PCR arrays were screened: pathways related to EMT signaling and the TGF-β/bone morphogenic protein (BMP), each on two independent biological replicates.
Soelch S., Beaufort N., Loessner D., Kotzsch M., Reuning U., Luther T., Kirchner T, & Magdolen V. (2021). Rab31-dependent regulation of transforming growth factor ß expression in breast cancer cells. Molecular Medicine, 27, 158.
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5

cDNA Synthesis and Wound Healing Gene Expression

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Prior to cDNA synthesis, RNA was adjusted to a final concentration of 1 μg RNA per μL of RNAse free water (Qiagen, Manchester, UK). Each sample was reverse transcribed with Random Primers (Promega, UK) and Bioscript Reverse Transcriptase (Bioline, Nottingham, UK). cDNA was plated into the 96 well RT2 Profiler PCR array plates (human wound healing gene panel, Qiagen) with Takyon SYBR mastermix (Eurogentec, Hampshire, UK). Plates were run on a CFX Connect thermal cycler using CFX Manager Software (Biorad, Hertfordshire, UK). R v.3.6.1 was used for t test comparisons (tNPWT vs sNPWT), while clustering was based on Euclidian distance and Ward D2's method using the R packages “RColorBrewer” and 'gplots'.21
Wilkinson H.N., Longhorne F.L., Roberts E.R., Brownhill V.R, & Hardman M.J. (2020). Cellular benefits of single‐use negative pressure wound therapy demonstrated in a novel ex vivo human skin wound model. Wound Repair and Regeneration, 29(2), 298-305.
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6

Investigating p53 Regulation of pH Homeostasis

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MDA-MB-157 cells stably expressing either p53-WT or p53-R273H were plated in 10-cm dishes and grown to ~50% confluency before beginning experimental modulation of pHi. To raise or lower pHi, medium was supplemented with 5 mM NH4Cl or 10 µM EIPA, respectively, for 48 hours. To induce a p53 response, 10 µM etoposide was added for the final 12 hours. Cells were harvested, and total RNA was extracted using the RNeasy Mini Kit (Qiagen). For each condition, 0.5 µg total RNA was used. Synthesis of complementary DNA was performed using the RT2 First Strand Synthesis Kit (Qiagen), and the 96-well RT2 Profiler PCR Array plates (Qiagen, PAHS-027ZA) were prepared according to the manufacturer’s instructions. The assay was performed on three independent preparations of cells for each condition. The RT2 PCR Array data sets were processed using the SAB PCR Array Data Analysis Web portal (http://pcrdataanalysis.sabiosciences.com/pcr/arrayanalysis.php), with a boundary cutoff of threefold increase in expression.
White K.A., Ruiz D.G., Szpiech Z.A., Strauli N.B., Hernandez R.D., Jacobson M.P, & Barber D.L. (2017). Cancer-associated arginine-to-histidine mutations confer a gain in pH sensing to mutant proteins. Science signaling, 10(495), eaam9931.
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7

Gene Expression Analysis in DENV-infected HFDPCs

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Total RNA was extracted from HFDPCs by using Trizol reagent (Thermo Fisher Scientific) as instructed in the protocol. Total RNA (1,000 ng) from each sample underwent cDNA synthesis by using the RT2 First Strand Kit (Qiagen, Valencia, CA). The resulting cDNA was mixed with H2O plus SYBR green dye, and then dispensed into a 96-well RT2 Profiler PCR array plate as described (Qiagen). DNA amplification was carried out using the Applied Biosystems StepONE Plus Real-Time PCR system (Thermo Fisher Scientific). The fold-change in gene expression in DENV-infected HFDPCs was relative to that of the untreated control. We considered a fold-change threshold of at least two-fold upregulation or downregulation.
The specific gene expression was also confirmed by RT-qPCR. cDNA was synthesized from 500 ng total RNA using Superscript III Reverse Transcriptase (Invitrogen). qPCR amplification was carried out with 3 ng of cDNA in 10 μl SYBR Green using the Applied Biosystems StepONE Plus Real-Time PCR system (Thermo Fisher Scientific). Transcript levels were normalized to that of glyceraldehyde 3-phosphate dehydrogenase (GAPDH). The primer sequences for gene detection are provided in Table S1.
Wei K.C., Huang M.S, & Chang T.H. (2018). Dengue Virus Infects Primary Human Hair Follicle Dermal Papilla Cells. Frontiers in Cellular and Infection Microbiology, 8, 268.
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8

Liver Tissue RNA Expression Analysis

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Total RNA was isolated from the frozen liver tissue samples using RNeasy Plus Mini Kit (Qiagen Pty Ltd, Chadstone, Vic., Australia) according to the manufacturer's instructions, with DNase treatment included; 1 μg of total RNA was reverse‐transcribed using RT2 First strand kit. The cDNA was then added to the RT2 SYBR green qPCR mastermix and loaded onto 96‐well RT2 Profiler PCR array plate (PARN‐030‐ZD; Qiagen Pty Ltd) and amplified on Bio‐Rad CFX Connect Real Time PCR Detection system for 40 cycles. PCR array data were analyzed according to the manufacturer's instructions. Relative gene expression was determined using the ∆∆Ct method normalized against five housekeeping genes, and the changes in gene expression were shown as a fold increase or decrease compared to control group.
Mohamad M., Mitchell S.J., Wu L.E., White M.Y., Cordwell S.J., Mach J., Solon‐Biet S.M., Boyer D., Nines D., Das A., Catherine Li S., Warren A., Hilmer S.N., Fraser R., Sinclair D.A., Simpson S.J., de Cabo R., Le Couteur D.G, & Cogger V.C. (2016). Ultrastructure of the liver microcirculation influences hepatic and systemic insulin activity and provides a mechanism for age‐related insulin resistance. Aging Cell, 15(4), 706-715.
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9

Inflammatory Response Gene Expression Profiling

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Total RNA from tongue tissues of WT and Mif−/− mice (N = 3 per group) was isolated using the RNeasy mini kit (Qiagen Valencia, CA, USA). RNA was reverse transcribed to cDNA using the RT2 HT First Strand kit (Qiagen Valencia, CA, USA). cDNA was applied to a RT2 profiler PCR Array plate containing a panel of mouse inflammatory response genes (Qiagen Valencia, CA, USA). Plates were run on a 7900HT Real-Time PCR System (Applied Biosystems, Foster City, CA, USA) using SYBR green for detection. Data were analyzed using the web-based RT2 profiler PCR Array data analysis software (www.SABiosciences.com/pcrarraydataanalysis.php).
Oghumu S., Knobloch T.J., Terrazas C., Varikuti S., Ahn-Jarvis J., Bollinger C.E., Iwenofu H., Weghorst C.M, & Satoskar A.R. (2016). Deletion of macrophage migration inhibitory factor inhibits murine oral carcinogenesis: Potential role for chronic pro-inflammatory immune mediators. International journal of cancer, 139(6), 1379-1390.
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10

Skin Transcriptome Analysis by qPCR

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The RNA of skin samples was isolated and purified with the RNeasy Plus Universal Mini Kit (Qiagen) according to the manufacturer’s protocol. cDNA synthesis was conducted with the RT2 First Strand Kit (Qiagen). cDNA was added together with RT2 SYBR Green Mastermix (Qiagen) into a customized 384-well RT2 Profiler PCR Array plate (Qiagen) with 48 genes (Table S1). Real-time PCR was conducted with a LightCycler 480® (Roche, Basel, Switzerland). The cycling conditions were programmed as recommended in the manufacturer’s protocol. The relative fold mRNA expression was calculated by the 2-ddCt-method using peptidylprolyl isomerase H as a housekeeping gene.
Riedl R., Kühn A., Rietz D., Hebecker B., Glowalla K.G., Peltner L.K., Jordan P.M., Werz O., Lorkowski S., Wiegand C, & Wallert M. (2023). Establishment and Characterization of Mild Atopic Dermatitis in the DNCB-Induced Mouse Model. International Journal of Molecular Sciences, 24(15), 12325.
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