Nsolver software v3

Manufactured by NanoString

Sourced in United States

NSolver software v3.0 is a data analysis software tool developed by NanoString. The core function of NSolver is to process and analyze data generated by NanoString's nCounter Analysis System. It provides users with the ability to perform advanced data normalization, statistical analysis, and visualization of gene expression data.

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Lab products found in correlation

Spss software v 21, by IBM (1 mentions) Amicon ultra ym 3 columns, by Merck Group (1 mentions) Mirneasy serum plasma kit, by Qiagen (1 mentions) Spss software v24, by IBM (1 mentions) Omics explorer v 3.2, by Qlucore (1 mentions)

4 protocols using nsolver software v3

Multivariate Analysis of Transcriptomic Data

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We used nSolver software v3.0 (NanoString Technologies) for the normalization of raw counts. Heat map and principle component analyses were performed on Qlucore Omics Explorer v3.2 (Lund, Sweden). Statistical analysis was performed using SPSS software v21.0 (IBM, Armonk, NY). All computed results having two-sided P value < 0.05 were considered significant.

Akhter A., Mughal M.K., Elyamany G., Sinclair G., Azma R.Z., Masir N., Shuib S., Rashid-Kolvear F., Shabani-Rad M.T., Stewart D.A, & Mansoor A. (2016). Multiplexed automated digital quantification of fusion transcripts: comparative study with fluorescent in-situ hybridization (FISH) technique in acute leukemia patients. Diagnostic Pathology, 11, 89.

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Profiling Serum miRNA by High-Content Analysis

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Human serum was isolated by centrifugation (2200g for 10 minutes at room temperature) from whole blood and snapfrozen. RNA was isolated from human and animal serum samples (200 μL) with the use of the miRNeasy Serum/Plasma Kit (Qiagen) according to the manufacturer’s instructions. Eluted RNA from serum samples was further purified and concentrated with the use of Amicon Ultra YM-3 columns (3000 kDa MWCO; Millipore).
For high-content miRNA analysis, RNAs after hybridization reactions were processed with the use of the nCounter Prep Station and nCounter Digital Analyzer. miRNA levels (n = 800) were analyzed with the use of the nSolver software v3.0 (Nanostring Technologies, Seattle, WA, USA). Normalization was performed with the use of all miRNAs (n = 110) with coefficients of variation <70%.^{14 (link)}Additional information is available in the Supplementary Methods.

Monaghan T.M., Seekatz A.M., Markham N.O., Yau T.O., Hatziapostolou M., Jilani T., Christodoulou N., Roach B., Birli E., Pomenya O., Louie T., Lacy D.B., Kim P., Lee C., Kao D, & Polytarchou C. (2021). Fecal Microbiota Transplantation for Recurrent Clostridioides difficile Infection Associates With Functional Alterations in Circulating microRNAs. Gastroenterology, 161(1), 255-270.e4.

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Immune Response Gene Expression Analysis

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Gene expression analysis was performed at NanoString Technologies (Seattle, WA, USA). RNA was used as input into the nCounter^® CAR T Characterization Gene Expression Panel (NanoString Technologies), a 770-plex gene expression panel that profiles the human immune response. Raw data were imported from the MAX digital analyzer into nSolver software v3.0 (NanoString Technologies). Standard quality control checks assessing imaging, binding density, positive control linearity and limit of detection were performed. By utilizing internal positive controls in the panels, raw gene expression data were first normalized. The messenger RNA (mRNA) data were further normalized by the geometric mean of a set of stably expressed reference genes. The mRNA expressed below background were filtered from the analysis using cutoffs of mean plus two standard deviations of negative controls.

Beider K., Itzhaki O., Schachter J., Grushchenko-Polaq A.H., Voevoda-Dimenshtein V., Rosenberg E., Ostrovsky O., Devillers O., Shapira Frommer R., Zeltzer L.A., Toren A., Jacoby E., Shimoni A., Avigdor A., Nagler A, & Besser M.J. (2022). Molecular and Functional Signatures Associated with CAR T Cell Exhaustion and Impaired Clinical Response in Patients with B Cell Malignancies. Cells, 11(7), 1140.

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Gene Expression Normalization and Analysis

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We used nSolver software v3.0 (NanoString Technologies) for the normalization of raw counts for various genes as determined by the NanoString nSolver platform. SPSS software v24.0 (IBM, Armonk, NY, USA) was utilized for other statistical evaluations. Hierarchical clustering and principal component analyses were performed employing Qlucore Omics Explorer v3.2 (Lund, Sweden). Results with fold change ≥2.0 and p-value < 0.05 were considered significant.

Elyamany G., Rizwan H., Akhter A., Aljabry M.S., Alotaibi S., Albalawi M.A., Shabani-Rad M.T., Roshan T.M, & Mansoor A. (2023). “Losing the Brakes”—Suppressed Inhibitors Triggering Uncontrolled Wnt/ß-Catenin Signaling May Provide a Potential Therapeutic Target in Elderly Acute Myeloid Leukemia. Current Issues in Molecular Biology, 45(1), 604-613.

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