Nsolver analysis software version 3

Manufactured by NanoString

Sourced in United States

NSolver analysis software version 3.0 is a data analysis tool designed for use with NanoString's nCounter Analysis System. The software provides a platform for processing, normalizing, and analyzing data generated from nCounter gene expression assays.

Automatically generated - may contain errors

Lab products found in correlation

Recoverall total nucleic acid isolation kit for ffpe, by Thermo Fisher Scientific (2 mentions) Ncounter elements assay, by NanoString (2 mentions) Rnase away, by Thermo Fisher Scientific (2 mentions) Ncounter analysis system, by NanoString (2 mentions) Nanodrop 2000, by Thermo Fisher Scientific (2 mentions) Rneasy mini kit, by Qiagen (2 mentions) Rneasy ffpe kit, by Qiagen (2 mentions) Ncounter gene expression assay, by NanoString (1 mentions) Agilent 2100 bioanalyzer, by Agilent Technologies (1 mentions) Facsaria cell sorter, by BD (1 mentions) Mouse cd4 t cell isolation kit, by Miltenyi Biotec (1 mentions) Rneasy plus mini kit, by Qiagen (1 mentions) Rneasy plus micro kit, by Qiagen (1 mentions) Ncounter pancancer immune profiling panel, by NanoString (1 mentions) Io360, by NanoString (1 mentions) Qiashredder, by Qiagen (1 mentions)

15 protocols using nsolver analysis software version 3

miRNA Expression Analysis Protocol

Cited 2 times

Check if the same lab product or an alternative is used in the 5 most similar protocols

miRNA data analysis was performed using the nSolver Analysis Software (version 3.0) freely available from NanoString Technologies. The global mean of top 100 miRNA expressers in the samples tested was used to content normalize the miRNA expression ac all samples as described previously [28 (link), 29 (link)].
Statistical analyses were performed with the R software [30 (link)]. Thirty miRNAs with average expression count > 10 were selected. Fold change > 2 was set as upregulation, and < -2 as downregulation. P values < .05 were considered statistically significant.

Kim E.N., Kim C.J., Kim S.R., Song J.A., Choe H., Kim K.B., Choi J.S, & Oh S.J. (2019). High serum CRP influences myocardial miRNA profiles in ischemia-reperfusion injury of rat heart. PLoS ONE, 14(5), e0216610.

+ Open protocol

+ Expand

FFPE RNA Extraction and Expression

Cited 1 time

Check if the same lab product or an alternative is used in the 5 most similar protocols

Three consecutive 20-μm curls cut from each FFPE block were immediately transferred to sterile microcentrifuge tubes and stored at room temperature. Microtome blades were then replaced, and equipment sterilization was performed with RNase AWAY (Life Technologies, Carlsbad, CA) between blocks. Xylene deparaffinization and RNA extraction of the curls were performed with use of the Recover All Total Nucleic Acid Isolation Kit for FFPE (Life Technologies). RNA concentration and purity were measured with the use of a Nano-Drop 2000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA). Gene expression was then quantified by using the nCounter Elements assay (NanoString Technologies) with the FFPE tissue–derived RNA isolates.^{24 (link),31 (link)} Quality control assessment and normalization were performed with nSolver Analysis Software version 3.0 (NanoString Technologies). The manufacturer-recommended default parameters for quality control flagging were used. Each sample was first normalized to the geometric mean of the positive controls (with default flagging of normalization factors <0.3 and >3), followed by normalization to the geometric mean of the housekeeping genes (with default flagging of normalization factors <0.1 and >10). RNA yields, quality controls, and reproducibility are previously reported.^{24 (link)}

Smith R.N., Matsunami M., Adam B.A., Rosales I.A., Oura T., Cosimi A.B., Kawai T., Mengel M, & Colvin R.B. (2018). RNA expression profiling of nonhuman primate renal allograft rejection identifies tolerance. American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons, 18(6), 1328-1339.

+ Open protocol

+ Expand

NanoString-Based Gene Expression Analysis

Check if the same lab product or an alternative is used in the 5 most similar protocols

NanoString data were normalized and analyzed using nSolver™ software. RNA ncounts were normalized using the geometric mean of five housekeeping genes including Cltc, Gapdh, Gusb, Hprt1, and Tubb5 using nSolver™ Analysis Software, version 3.0 (NanoString Technologies, Inc.). A cutoff was introduced at the value two‐fold of the highest negative control present on the chip. Fold changes were calculated using the average of each group. For each experiment, the fold changes were calculated comparing the experimental group to their appropriate controls. To compare the normalized gene expression levels in Grn^−/− and wt mice, unpaired two‐tailed Student's t‐test was performed (*P < 0.05, **P < 0.01, ***P < 0.001). The volcano blot was generated employing GraphPad Prism 7 software. The heatmap was generated employing Multi Experiment Viewer v 4.9. The expression value for each gene was normalized to the mean value of wt mice followed by a log2 transformation.

Götzl J.K., Brendel M., Werner G., Parhizkar S., Sebastian Monasor L., Kleinberger G., Colombo A., Deussing M., Wagner M., Winkelmann J., Diehl‐Schmid J., Levin J., Fellerer K., Reifschneider A., Bultmann S., Bartenstein P., Rominger A., Tahirovic S., Smith S.T., Madore C., Butovsky O., Capell A, & Haass C. (2019). Opposite microglial activation stages upon loss of PGRN or TREM2 result in reduced cerebral glucose metabolism. EMBO Molecular Medicine, 11(6), e9711.

+ Open protocol

+ Expand

Normalizing Gene Expression Data

Check if the same lab product or an alternative is used in the 5 most similar protocols

Gene expression data was analysed using the nSolver™ Analysis Software version 3.0 from NanoString Technologies (NanoString Technologies, WA, USA). Raw data was normalised by subtracting the geometric mean of six negative controls while technical variation was normalised through internal positive controls. A transcript was considered not detected if its mean count was below the geometric mean of the negative control counts.

Huang B., West N.P., Vider J., Cox A.J., Constantino T., Harrower B.J., Pyke A.T., McMahon J., Northill J.A., Riordan T, & Warrilow D. (2017). Diagnosis and typing of influenza using fluorescent barcoded probes. Scientific Reports, 7, 18092.

+ Open protocol

+ Expand

NanoString Gene Expression Profiling of Macaca fascicularis

Check if the same lab product or an alternative is used in the 5 most similar protocols

Oligonucleotide probes specific to Macaca fascicularis were manufactured for the mRNA sequences of 38 genes (Integrated DNA Technologies, Coralville, IA). These included a previously-described AMR 34-gene-set comprised of 18 endothelial, 6 NK cell, and 10 inflammation-related genes, as well as 4 housekeeping genes (12 (link)). Probe sequences are provided in Table S1. Gene expression was then quantified with the NanoString® nCounter® Gene Expression assay (NanoString Technologies, Seattle, WA) as per manufacturer instructions. To assess reproducibility, eight samples were randomly selected for duplicate analysis in separate runs. Quality control assessment and normalization of raw NanoString® gene expression results were performed with nSolver™ Analysis Software Version 3.0 (NanoString Technologies, Seattle, WA) using the manufacturer-recommended default parameters.

Adam B.A., Smith R.N., Rosales I.A., Matsunami M., Afzali B., Oura T., Cosimi A.B., Kawai T., Colvin R.B, & Mengel M. (2017). Chronic Antibody-Mediated Rejection in Nonhuman Primate Renal Allografts: Validation of Human Histological and Molecular Phenotypes. American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons, 17(11), 2841-2850.

+ Open protocol

+ Expand

Comprehensive Gene Expression Profiling

Check if the same lab product or an alternative is used in the 5 most similar protocols

Total RNA was extracted from cell lines using a QIAGEN RNeasy Mini Kit (QIAGEN, Hilden, Germany; Cat #74104) following the manufacturer's protocol. An Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA, USA) was used to check the quality and quantity of extracted RNA from samples. Only RNA with length greater than 300 nucleotides (i.e. functional RNA) was considered for quantity calculations for downstream use. Aliquots (100 ng) of unamplified total RNA were hybridized with the NanoString PanCancer Pathway CodeSet and Capture ProbeSet (NanoString Technologies Inc., Seattle, WA, USA) at 65 °C for at least 16 h but not more than 48 h in a thermal cycler. The hybridized RNA samples were then loaded onto the NanoString nCounter system for gene expression analysis. Gene expression normalization of NanoString data was performed using nSolver analysis software version 3.0 (NanoString Technologies Inc.). The raw counts from NanoString were subjected to background subtraction, positive control normalization, and reference gene normalization. The normalized counts were then log2‐transformed prior to downstream analysis.

Sundararajan V., Tan T.Z., Lim D., Peng Y., Wengner A.M., Ngoi N.Y., Jeyasekharan A.D, & Tan D.S. (2022). Nuclear pCHK1 as a potential biomarker of increased sensitivity to ATR inhibition. The Journal of Pathology, 259(2), 194-204.

+ Open protocol

+ Expand

Immune Gene Expression Profiling of OCCC

Check if the same lab product or an alternative is used in the 5 most similar protocols

Gene expression profiling of the OCCC samples on the Pan‐Cancer Immune Panel was retrieved. The NanoString Pan‐Cancer Immune Panel analysed the expression levels of 730 genes related to immune cell types, CT antigens, responses, and functions. Gene expression normalization of NanoString data was performed using nSolver analysis software version 3.0 (NanoString Technologies Inc). Only samples that passed all quality metrics were retained for analysis (supplementary material, Table S1). The raw NanoString counts were subjected to background subtraction, positive control normalization, and 40‐reference gene normalization. The normalized counts were then log2‐transformed prior to downstream analysis.

Heong V., Tan T.Z., Miwa M., Ye J., Lim D., Herrington C.S., Iida Y., Yano M., Yasuda M., Ngoi N.Y., Wong S.J., Okamoto A., Gourley C., Hasegawa K., Tan D.S, & Huang R.Y. (2021). A multi‐ethnic analysis of immune‐related gene expression signatures in patients with ovarian clear cell carcinoma. The Journal of Pathology, 255(3), 285-295.

+ Open protocol

+ Expand

Isolation and Analysis of Colonic LPLs

Check if the same lab product or an alternative is used in the 5 most similar protocols

LPLs were isolated as described above from distal colons of naïve mice or from mice infected with C. rodentium 9 days p.i. The colonic LPL were FACS-sorted into CD4⁺ T cells (EpCAM^-CD45⁺CD3⁺CD4⁺) by using a FACSAria cell sorter (Becton Dickinson). Splenic CD4⁺ T cells were purified (≥95% purity) using negative selection with a mouse CD4⁺ T cell isolation kit (Miltenyi Biotec, Auburn, CA) and total RNA was isolated from CD4⁺ T cells using a Qiagen RNeasy Plus Micro Kit (Qiagen, Hilden, Germany). In some experiments total RNA from whole distal colons was isolated using a Qiagen RNeasy Plus Mini Kit (Qiagen, Hilden, Germany) and used as the source of RNA for further analysis. Total RNA (100 ng) was used as samples for probe-based NanoString system (nCounter XT Code Set; Seattle, WA, USA). The raw data for each gene was compile and normalized against the spike-in positive (6 genes) and negative (8 genes) internal reference genes and were expressed as normalized counts by using the nSolver analysis software version 3.0 (NanoString Technologies). The gene expression data were further normalized to the geometric mean of the expression of internal reference genes and presented as normalized counts/gene/biological sample.

Solaymani-Mohammadi S, & Berzofsky J.A. (2019). Interleukin 21 collaborates with interferon-γ for the optimal expression of interferon-stimulated genes and enhances protection against enteric microbial infection. PLoS Pathogens, 15(2), e1007614.

+ Open protocol

+ Expand

Transcriptomic Profiling of Pulmonary Autopsy

Cited 1 time

Check if the same lab product or an alternative is used in the 5 most similar protocols

RNA was isolate from tissue samples using the Maxwell RNA extraction system (Promega, Madison, Wisconsin). mRNA expression data of pulmonary autopsy specimens was obtained via the nCounter Analysis System (NanoString Technologies, Seattle, WA) using the PanCancer Progression Panel (770 genes including 30 reference genes). Normalization of raw counts was performed using the nSolver analysis software version 3.0 (NanoString Technologies, Seattle, WA) and a modified version of the nCounter advanced analysis module (version 1.1.5). The normalization process included positive normalization (geometric mean), negative normalization (arithmetic mean) and reference normalization (geometric mean) using the 5 most suitable reference genes from the total of 30 available reference genes selected by the geNorm algorithm [73 (link)]. Further analysis of the resulting log2 mRNA counts was performed using custom R code. A Shapiro-Wilks test was performed on all intra-group gene expressions which showed that the vast majority of expression data is normally distributed (>85%, α = 0.05). Raw counts and normalised data for analyzed genes are found in S3 Table.

Lee A.J., Feng E., Chew M.V., Balint E., Poznanski S.M., Giles E., Zhang A., Marzok A., Revill S.D., Vahedi F., Dubey A., Ayaub E., Jimenez-Saiz R., McGrath J.J., Ritchie T.M., Jordana M., Jonigk D.D., Ackermann M., Ask K., Miller M., Richards C.D, & Ashkar A.A. (2022). Type I interferon regulates proteolysis by macrophages to prevent immunopathology following viral infection. PLoS Pathogens, 18(5), e1010471.

+ Open protocol

+ Expand

FFPE RNA Extraction and Analysis

Check if the same lab product or an alternative is used in the 5 most similar protocols

Three consecutive 20-μm curls cut from each FFPE block were immediately transferred to sterile microcentrifuge tubes and stored at room temperature. Microtome blades were then replaced and equipment sterilization with RNase AWAY (Life Technologies, Carlsbad, CA, USA) between blocks. Curls Xylene deparaffinization and RNA extraction were performed with the RecoverAll™ Total Nucleic Acid Isolation Kit for FFPE (Life Technologies, Carlsbad, CA, USA). RNA concentration and purity were measured with a Nano-Drop 2000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA). Gene expression was then quantified using the nCounter Elements assay (NanoStringTechnologies) with the FFPE tissue derived RNA isolates (17 (link), 19 ). Quality control assessment and normalization were performed with nSolver Analysis Software version 3.0 (NanoString Technologies). The manufacturer recommended default parameters for quality control flagging were used. Each sample was first normalized to the geometric mean of the positive controls (with default flagging of normalization factors <0.3 and >3), followed by normalization to the geometric mean of the house keeping genes (with default flagging of normalization factors <0.1 and >10).

Smith R.N., Adam B.A., Rosales I.A., Matsunami M., Oura T., Cosimi A.B., Kawai T., Mengel M, & Colvin R.B. (2018). RNA EXPRESSION PROFILING OF RENAL ALLOGRAFTS IN A NON-HUMAN PRIMATE IDENTIFIES VARIATION IN NK AND ENDOTHELIAL GENE EXPRESSION. American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons, 18(6), 1340-1350.

+ Open protocol

+ Expand

About PubCompare

Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.

We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.

However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.

Ready to get started?

Revolutionizing how scientists
search and build protocols!