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Ncounter master kit

Manufactured by NanoString
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The NCounter Master Kit is a comprehensive package designed for gene expression analysis. It provides the necessary components to perform sensitive, accurate, and multiplexed measurement of gene expression levels using NanoString's nCounter technology.

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Lab products found in correlation

Nsolver 4.0 analysis software, by NanoString (2 mentions) Ncounter advanced analysis module v 2, by NanoString (1 mentions) Allprep dna rna mini kit, by Qiagen (1 mentions) Ncounter analysis system, by NanoString (1 mentions) Nsolver analysis software v4, by NanoString (1 mentions) Low rna input kit, by NanoString (1 mentions) Rneasy micro kit, by Qiagen (1 mentions) Capture probeset, by NanoString (1 mentions) Reporter codeset, by NanoString (1 mentions) Qiashredder kit, by Qiagen (1 mentions) Ncounter mouse pancancer immune profiling panel, by NanoString (1 mentions) Ncounter mouse pancancer pathways panel, by NanoString (1 mentions) Ncounter flex system, by NanoString (1 mentions) Rneasy plus micro kit, by Qiagen (1 mentions) Ds 11 spectrophotometer, by DeNovix (1 mentions) Ncounter technology, by NanoString (1 mentions) Ncounter low rna input kit, by NanoString (1 mentions) Ncounter dxprep station, by NanoString (1 mentions) Ncounter dx digital analyzer, by NanoString (1 mentions) Paxgene blood rna kit, by Qiagen (1 mentions)

6 protocols using ncounter master kit

1

Colonic RNA and DNA Extraction

Cited 1 time
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Colonic mucosal RNA and DNA was isolated using AllPrep DNA/RNA Mini Kit (Qiagen, Catalog No. 80204) using the protocol previously described (Harrison et al., 2018 (link)). The protocol was slightly modified to include a bead-beating step. Expression of inflammation-related genes was assessed using nCounter Inflammation Panel (Mouse v2) codecs, nCounter Master Kit (NanoString Technologies, Seattle, WA), and the NanoString nCounter® Analysis System at the University of Arizona Genetics Core facility. Data were analyzed using nSolver Analysis software v4.0 with the nCounter Advanced Analysis module v. 2.0.115 (NanoString Technologies).
Yu S., Balasubramanian I., Laubitz D., Tong K., Bandyopadhyay S., Lin X., Flores J., Singh R., Liu Y., Macazana C., Zhao Y., Béguet-Crespel F., Patil K., Midura-Kiela M.T., Wang D., Yap G.S., Ferraris R.P., Wei Z., Bonder E.M., Häggblom M.M., Zhang L., Douard V., Verzi M.P., Cadwell K., Kiela P.R, & Gao N. (2020). Paneth cell-derived lysozyme defines the composition of mucolytic microbiota and the inflammatory tone of the intestine. Immunity, 53(2), 398-416.e8.
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2

RiboTag-based Polyribosome Immunoprecipitation

Cited 2 times
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Polyribosome immunoprecipitation was achieved as described in 14 (link), 33 (link). Briefly, pooled tissue from RiboTag (RT)+/+ mice with virally mediated Cre expression in VP→MDT neurons (n= 4–5 mice per sample) was homogenized and 800-μL of the supernatant was incubated in HA-coupled magnetic beads (Invitrogen: 100.03D; Covance: MMS-101R) overnight at 4°C. Magnetic beads were then washed in high salt buffer. Following TRK lysis buffer addition, RNA was extracted with the RNeasy Micro kit (Qiagen: 74004). For input, 50 ng of RNA was used and 1–2 ng of RNA from immunoprecipitated samples were amplified using the Low RNA Input kit (NanoString Technologies®). All samples were then processed with the nCounter Master Kit (NanoString Technologies®) by UMSOM IGS on a custom-made gene expression Code set (see Supplementary Table 3 for primer sequences). Data were analyzed with nSolver Analysis software 14 (link).
Engeln M., Fox M.E., Chandra R., Choi E.Y., Nam H., Qadir H., Thomas S.S., Rhodes V.M., Turner M.D., Herman R.J., Calarco C.A, & Lobo M.K. (2022). Transcriptome profiling of the ventral pallidum reveals a role for pallido-thalamic neurons in cocaine reward. Molecular psychiatry, 27(10), 3980-3991.
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3

Transcriptional Profiling of Sorted Tumor Cells

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Total RNA from sorted CD45− tumor cells was extracted using a QIAshredder kit (QIAGEN) and an RNeasy Plus Micro Kit (QIAGEN) according to the manufacturer’s protocol. RNA quantification was performed using the DeNovix DS-11 Spectrophotometer (DeNovix, Inc). 100 ng of purified RNA was added to 3 μL of Reporter CodeSet and 2 μL Capture ProbeSet using an nCounter master kit as recommended (NanoString Technologies). Samples were processed on the NanoString nCounter Flex System per manufacturer instructions using the nCounter Mouse PanCancer Immune Profiling panel or the nCounter Mouse PanCancer Pathways panel (NanoString Technologies). Each gene set interrogates 750 cancer-related genes alongside 20 internal reference controls (full gene list and controls available on manufacturer’s website). Differentially expressed genes were identified in nSolver 4.0 Analysis Software (NanoString) as genes with a p value of less than 0.05 versus the respective baseline control. Reactome pathway analysis was performed using the NetworkAnalyst. The NanoString data have been deposited in the NCBI GEO under accession number GSE178135.
Dixon M.L., Luo L., Ghosh S., Grimes J.M., Leavenworth J.D, & Leavenworth J.W. (2021). Remodeling of the tumor microenvironment via disrupting Blimp1+ effector Treg activity augments response to anti-PD-1 blockade. Molecular Cancer, 20, 150.
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4

Nanostring Gene Expression Analysis

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Total mRNA (15μl) were analyzed using the nCounter Master Kit from NanoString Technologies (NanoString Technologies, Inc Seattle, WA). Gene Expression CodeSets of our interest for the nCounter Analysis System were preordered from NanoString Technologies, Inc (www.nanostring.com). The nCounter Analysis System is an integrated system comprised of a fully-automated Prep Station, a Digital Analyzer, and the CodeSet (molecular barcodes) reader.
Lo W.C., Arsenescu V., Arsenescu R.I, & Friedman A. (2016). Inflammatory Bowel Disease: How Effective Is TNF-α Suppression?. PLoS ONE, 11(11), e0165782.
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5

Measuring Gene Expression via NanoString nCounter

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The nCounter technology from NanoString measure gene expression at the RNA level. NanoString reactions were performed in technical duplicates on the 4 biological replicates used for RNA-seq plus 1 independent fifth replicate. About 1 ng of RNA from input and IP samples was used for preamplification with the nCounter Low RNA Input Kit (NanoString Technologies, WA) to obtain sufficient cDNA to be run on the Counter platform (NanoString Technologies) (Primers for preamplification are listed in S14 Table). A Custom CodeSets for 28 targets including 4 housekeeping genes was designed (probes listed in S14 Table), and the samples were run with the nCounter Master Kit (NanoString Technologies) following the manufacturer’s protocol. Preamplification, nanoString reactions, and quality check steps were performed at the Institute for Genome Sciences, University of Maryland School of Medicine. Normalization to housekeeping genes and data analysis was performed using the nSolver 4.0 analysis software (NanoString).
Udagawa T., Atkinson P.J., Milon B., Abitbol J.M., Song Y., Sperber M., Huarcaya Najarro E., Scheibinger M., Elkon R., Hertzano R, & Cheng A.G. (2021). Lineage-tracing and translatomic analysis of damage-inducible mitotic cochlear progenitors identifies candidate genes regulating regeneration. PLoS Biology, 19(11), e3001445.
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6

Nanostring Transcriptomic Profiling of Tumor RNA

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Total RNA was purified from excised tumors using the RNeasy Mini kit (Qiagen). RNA from whole blood was was isolated using the Paxgene blood RNA kit (Qiagen). RNA quality was assessed using Bioanalyzer 2100 (Agilent) and final concentration determined by Qubit (Life Technologies). For nanostring analysis, 100 ng of purified RNA was added to 3 μL of Reporter CodeSet and 2 μL Capture ProbeSet using an nCounter master kit as recommended (NanoString Technologies). Samples were processed the following day using the nCounter DxPrep Station and nCounter Dx Digital Analyzer (NanoString Technologies). Data was analyzed using nSolver 2.6 software. Heat maps were created using Cluster 3.0 and Java TreeView-1.1.6r4.
McCaw T.R., Li M., Starenki D., Cooper S.J., Liu M., Meza-Perez S., Arend R.C., Buchsbaum D.J., Forero A, & Randall T.D. (2018). The expression of MHC class II molecules on murine breast tumors delays T cell exhaustion, expands the T cell repertoire and slows tumor growth. Cancer immunology, immunotherapy : CII, 68(2), 175-188.
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