Total RNA extracted from mouse brain was purified using TRIzol and RNAqueous kit (Ambion, Thermo Fisher Scientific, Waltham, MA, USA) and reverse transcribed using Superscript III (Invitrogen, Life Technologies, Carlsbad, CA, USA). Multiplex analysis of RNA was done using the nCounter GX mouse inflammation kit (NanoString Technologies, Seattle, WA, USA) and a custom Neurodegeneration kit [13 (link)] using 100 ng total RNA from mouse brains.
Ncounter gx mouse inflammation kit
Manufactured by NanoString
Sourced in United States
The NCounter GX mouse inflammation kit is a laboratory tool designed to measure the expression levels of a panel of genes related to inflammation in mouse samples. The kit provides a standardized and efficient method for quantifying the expression of these genes, enabling researchers to gain insights into inflammatory processes in mouse models.
Automatically generated - may contain errors
Lab products found in correlation
Superscript 3, by Thermo Fisher Scientific (1 mentions)
Icycler, by Bio-Rad (1 mentions)
Sybr green 1 system, by Bio-Rad (1 mentions)
Nsolver analysis software, by NanoString (1 mentions)
Trizol, by Thermo Fisher Scientific (1 mentions)
Ncounter system, by NanoString (1 mentions)
Rnalater, by Merck Group (1 mentions)
Jmp genomics, by SAS Institute (1 mentions)
6 protocols using ncounter gx mouse inflammation kit
1
Multiplex Analysis of Neuroinflammation and Neurodegeneration
2
Comprehensive Mouse Inflammation Gene Analysis
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The nCounter GX Mouse Inflammation Kit (Nanostring, Seattle, USA) was used to measure a comprehensive set of 248 inflammation related mouse genes and six internal reference genes.
3
Profiling Inflammatory Gene Expression
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RNA was isolated and reverse transcribed as described [9 (link)]. Inflammatory gene expression was profiled using nCounter GX mouse inflammation kit consisting of 184 inflammation-related genes and 6 internal reference genes and analyzed by nSolver software 2.6 (NanoString Technologies) as directed by the manufacturer [18 ]. The in silico analysis for the NOR1 consensus NBRE (NGFI-B response element) motif within differentially regulated genes was performed using the MatInspector software (Genomatix Inc., Ann Arbor, MI). Real-time RT-PCR was performed with the iCycler and SYBR Green I system (Bio-Rad, Hercules, Calif). Each sample was analyzed in triplicate and normalized to transcription factor IIB (TFIIB) mRNA expression, and data was calculated using the 2-ΔΔCt method [19 (link)]. Sequences of the primers for RT-PCR were as follows: NOR1 Forward 5′-GGCCGCAGCTGCACTCAGTC -3, Reverse 5′-GCGGAGGGAAGGTCAGCGTG -3′; TFIIB Forward: 5′-CTCTCCCAAGAGTCACATGTCC-3′, Reverse: 5′-CAATAACTCGGTCCCCTACAAC-3′.
4
Inflammation Gene Expression Profiling
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nCounter GX Mouse Inflammation Kit from NanoString Technologies (Seattle, WA) was applied to test a comprehensive set of 179 inflammation-related genes in this study. The mouse probe sequences were screened against mouse RefSeq to eliminate potentially cross-hybridizing probes. Total RNA (100 ng) was hybridized to nCounter™ capture and reporter probes at 65 °C for 16 h. The hybridized products were purified and processed using an automated sample prep station, and the images were prepared using the NanoString Digital Analyzer according to the company’s standard gene expression assay protocol [http://www.nanostring.com ]. The 179 mouse inflammation-related genes and 6 internal reference genes are detailed in Additional file 1 : Table S2.
5
Macrophage Inflammatory Responses in NOR1-Deficient Mice
6
Gene Expression Analysis of Colon Inflammation
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Colon tissues, approximately 2 cm long, and 1 cm away from the rectum were rinsed thoroughly by PBS and stored in RNAlater (Sigma-Aldrich, St. Louis, MO) at −80 °C. Six randomly selected colonic tissues from 50 mg/kg standard and ETO- curcumin groups as well as their respective non-treatment and DSS-treatment control groups were used for the gene expression analysis. The nCounter GX mouse inflammation kit (Nanostring Technologies, Seattle, WA) was used to determine gene expression alterations in inflammation-associated genes. In brief, RNA extracts from colon tissues were subjected to nCounter RNA sample preparation. Thereafter, 100 ng of RNA was used to hybridize probes at 65 °C for 18 hours, followed by purification and analysis on an nCounter Prep Station and Digital Analyzer. The raw data were normalized using nSolver (Nanostring Technologies) using built-in positive controls and the housekeeping genes were used to normalize and calculate mRNA content. Data were then analyzed by multiple t-test with correction for multiple comparison using Sidak-Bonferroni methods using JMP genomics (SAS, Cary, NC).
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