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Ncounter sprint profiler

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The NCounter SPRINT Profiler is a compact, benchtop instrument designed for rapid and efficient gene expression analysis. The core function of the NCounter SPRINT Profiler is to perform digital molecular barcoding and high-throughput counting of target molecules within a biological sample, enabling sensitive and quantitative measurement of gene expression levels.

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Lab products found in correlation

Nsolver 4, by NanoString (8 mentions) Nsolver analysis software, by NanoString (7 mentions) Ncounter sprint cartridge, by NanoString (4 mentions) Rneasy mini kit, by Qiagen (4 mentions) Nanodrop spectrophotometer, by Thermo Fisher Scientific (4 mentions) Nhpv2 immunology reporter and capture probesets, by NanoString (3 mentions) Ncounter mouse inflammation v2 panel, by NanoString (3 mentions) Ncounter human immunology v2 panel, by NanoString (3 mentions) Trizol reagent, by Thermo Fisher Scientific (3 mentions) Advanced analysis 2, by NanoString (2 mentions) Nsolver analysis software version 4, by NanoString (2 mentions) Covid 19 pluspanel plus kit, by NanoString (2 mentions) Rneasy ffpe kit, by Qiagen (2 mentions) Bioanalyzer, by Agilent Technologies (2 mentions) Ncounter advanced analysis 2, by NanoString (2 mentions) Nanodrop 2000, by Thermo Fisher Scientific (2 mentions) Qubit 2.0 fluorometer, by Thermo Fisher Scientific (2 mentions) Rneasy plus mini kit, by Qiagen (2 mentions) Rlt buffer, by Qiagen (2 mentions) Ncounter human immunology v2 gene expression code set, by NanoString (1 mentions)

Spelling variants of this product

NCounter™ SPRINT (19 citations) NanoString nCounter SPRINT Profiler machine (2 citations) NCounter SPRINT Profiler analytical system (2 citations)

70 protocols using ncounter sprint profiler

1

Nanostring Immunology Gene Expression

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Gene expression was measured on the nanoString nCounter SPRINT Profiler (NanoString Technologies) using the nCounter Human Immunology v2 gene expression Code Set (NanoString Technologies). Samples were prepared and processed according to the manufacturer’s recommendations. Briefly, 50 ng total RNA was hybridized in solution to the nCounter Human Immunology v2 gene expression Code Set for 18 h at 65°C. Hybridized samples were then loaded into the nCounter SPRINT cartridge (NanoString Technologies), which was then sealed and placed in the instrument for processing and analysis.
SINGH N., HOFMANN T.J., GERSHENSON Z., LEVINE B.L., GRUPP S., TEACHEY D.T, & BARRETT D.M. (2017). Monocyte lineage-derived IL-6 does not affect chimeric antigen receptor T-cell function. Cytotherapy, 19(7), 867-880.
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2

Gene Expression Analysis of FFPE Samples

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The PanCancer IO360 Gene Expression Panel 31 (750 targeted and 20 reference genes) was used to assess whether perfusion affected targeted (immuno‐oncology) gene expression. This technology works robustly on small quantities of formalin‐fixed, paraffin‐wax embedded (FFPE) tissue, which complied with study ethics. For each sample, 100–400 ng of RNA was analysed; this was calculated as 80 ng of RNA adjusted for the % of RNA fragments consisting of 50–300 nucleotides of the total RNA. Samples were run on the NanoString® nCounter® SPRINT Profiler (NanoString® Technologies, Seattle, WA, USA) according to the manufacturer's protocols.
Barrow‐McGee R., Procter J., Owen J., Woodman N., Lombardelli C., Kothari A., Kovacs T., Douek M., George S., Barry P.A., Ramsey K., Gibson A., Buus R., Holgersen E., Natrajan R., Haider S., Shattock M.J., Gillett C., Tutt A.N., Pinder S.E, & Naidoo K. (2019). Real‐time ex vivo perfusion of human lymph nodes invaded by cancer (REPLICANT): a feasibility study. The Journal of Pathology, 250(3), 262-274.
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3

Breast Cancer Gene Expression Profiling

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Gene expression was measured using the NanoString Breast Cancer 360 assay (BC360TM) on an NanoString nCounter® SPRINT Profiler (NanoString Technologies Inc., Seattle, WA, USA). The BC360 assay covers genes from 33 independent signatures, including the PAM50 signature (https://www.nanostring.com/, accessed date: 30 August 2019). By using multiplexed hybridization and digital readouts of fluorescent barcoded probes, the NanoString platform measures the relative abundance of each mRNA transcript of interest [20 (link)]. In a single reaction, the BC360TM gene expression panel (including 758 gene-specific probe pairs of the BC360 targets, 18 housekeeping genes used for normalization, 6 exogenous positive control RNA targets, and 8 exogeneous negative control sequences) was hybridized in solution with 50–250 ng total RNA overnight (24 h) at 65 °C. The samples were processed using the NanoString nCounter® SPRINT platform in accordance with the instructions and kits provided by NanoString Technologies (https://www.nanostring.com/, accessed date: 30 August 2019).
Jørgensen C.L., Larsson A.M., Forsare C., Aaltonen K., Jansson S., Bradshaw R., Bendahl P.O, & Rydén L. (2021). PAM50 Intrinsic Subtype Profiles in Primary and Metastatic Breast Cancer Show a Significant Shift toward More Aggressive Subtypes with Prognostic Implications. Cancers, 13(7), 1592.
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4

RNA Extraction and NanoString Analysis for Sepsis

Cited 4 times
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PAXgene Blood RNA samples were shipped to Inflammatix (Burlingame, CA, USA) and processed by technicians blinded to clinical outcomes. Briefly, RNA extraction from PAXgene Blood RNA was performed in batched mode using a standardized protocol on the QiaCube® as previously described [16 (link)].
The InSep test consists of 29 target mRNAs composed of three separate, validated sub-panels: the 11-mRNA “Sepsis MetaScore” [13 (link)], 7-mRNA “Bacterial-Viral MetaScore” [14 (link)], and 11-mRNA “Stanford mortality score” [12 (link)], and has been described elsewhere [11 (link)]. RNA targets were counted using the NanoString nCounter® SPRINT Profiler from 150 ng of isolated RNA; the expression of four housekeeping genes (CDIPT, KPNA6, RREB1, YWHAB) was normalized using geometric-mean gene normalization, i.e., for each sample, counts for all genes were multiplied by a sample-specific factor such that the geometric means of housekeeping gene counts become equal across all samples [16 (link)]. In the current study, we applied the Bacterial Viral Non-infected (BVN)-2 algorithm of the InSep test [17 ]. The IMX-BVN-2 classifier was directly applied to the NanoString data, blinded to clinical outcomes.
Safarika A., Wacker J.W., Katsaros K., Solomonidi N., Giannikopoulos G., Kotsaki A., Koutelidakis I.M., Coyle S.M., Cheng H.K., Liesenfeld O., Sweeney T.E, & Giamarellos-Bourboulis E.J. (2021). A 29-mRNA host response test from blood accurately distinguishes bacterial and viral infections among emergency department patients. Intensive Care Medicine Experimental, 9, 31.
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5

Whole Blood Transcriptomic Profiling

Cited 1 time
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Whole blood (2.5 mL) was collected in PAXgene Blood RNA tubes (PreAnalytics, Hombrechtikon, Switzerland) on the day of inclusion, and subsequently aliquoted and stored at −80 °C until analysis. To perform target gene amplification and generate IMX-SEV-3b classifier results, the samples were shipped on dry ice to the Inflammatix laboratory (Burlingame, CA, USA) in batches, following the procedure previously described [29 (link)]. RNA was extracted from PAXgene tubes using the RNeasy® Plus Micro Kit (QIAGEN, Hilden, Germany) on the QiaCube® Connect instrument. The NanoString nCounter® SPRINT profiler (NanoString, Seattle, WA, USA) was then used to quantify the 29 host target mRNAs, as well as four housekeeping genes for normalization (CDIPT, KPNA6, RREB1 and YWHAB) from 150 ng of isolated RNA. RNA concentrations were determined for 29 genes of various aspects of the immune response and included CEACAM1, ZDHHC19, C9orf95, GNA15, BATF, C3AR1, KIAA1370, TGFBI, MTCH1, RPGRIP1, HLA-DPB1, HK3, TNIP1, GPAA1, CTSB, IFI27, JUP, LAX1, DEFA4, CD163, RGS1, PER1, HIF1A, SEPP1, C11orf74, CIT, LY86, TST and KCNJ2 [29 (link)]. Operators at Inflammatix were blinded to all other study results, and the NanoString data were subjected to direct application of the SEV-3b classifier, blinded to clinical outcomes.
Daenen K., Tong-Minh K., Liesenfeld O., Stoof S.C., Huijben J.A., Dalm V.A., Gommers D., van Gorp E.C, & Endeman H. (2023). A Transcriptomic Severity Classifier IMX-SEV-3b to Predict Mortality in Intensive Care Unit Patients with COVID-19: A Prospective Observational Pilot Study. Journal of Clinical Medicine, 12(19), 6197.
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6

Irradiation-Induced Immune Gene Expression

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Tumors were resected from WT and Sirpα−/− mice 12 h and 18 h after 8 Gy IR (n = 2 mice per time point), followed by isolation of total RNA with TRIzol Reagent (The Invitrogen Life Technologies). RNA samples of the two-time points were pooled, of which 100 ng RNA was used for gene expression detection with the NanoString Mouse Immunology Panel. The nCounter XT protocol was used for hybridization and the data was collected by the Nanostring nCounter® SPRINT Profiler followed by analyses with nSolver 2.6 software (NanoString Technologies). Background hybridization by spiked-in negative controls was deducted. A normalization factor was calculated from the spiked-in exogenous positive controls in each sample and applied to the raw counts from nCounter™ output data. The complete gene expression profiling data have been deposited in the Gene Expression Omnibus (GEO) database under accession code GSE149882.
Bian Z., Shi L., Kidder K., Zen K., Garnett-Benson C, & Liu Y. (2021). Intratumoral SIRPα-deficient macrophages activate tumor antigen-specific cytotoxic T cells under radiotherapy. Nature Communications, 12, 3229.
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7

Karyotyping of hiPSC Lines Using NanoString

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Karyotypes of hiPSC lines were tested with the NanoString nCounter Elements technology with a customized NanoString Probe Set based on nCounter® Human Karyotype Panel following the manufacturer’s advice. In short, 200 ng gDNA was fragmented by AluI digestion. After hybridization with the Capture and Reporter Probe Set at 65 °C, the samples were analyzed on the nCounter® Sprint Profiler (NanoString Technologies, Seattle, WA, USA) and evaluated based on the manufacturer’s protocol for copy number variation (CNV).
Kayser A., Dittmann S., Šarić T., Mearini G., Verkerk A.O, & Schulze-Bahr E. (2023). The W101C KCNJ5 Mutation Induces Slower Pacing by Constitutively Active GIRK Channels in hiPSC-Derived Cardiomyocytes. International Journal of Molecular Sciences, 24(20), 15290.
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8

Quantifying Immune Gene Expression Using NanoString

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NHPV2_Immunology reporter and capture probe sets (NanoString Technologies) were hybridized with 5 μl of each RNA sample at 65°C for at least 12 h. The RNA-probe set complexes were then loaded into an nCounter microfluidics cartridge and assayed on a NanoString nCounter SPRINT Profiler. To estimate the abundance of each of the 769 unique mRNA targets included in the NHPV2_Immunology panel, fluorescent reporter barcodes were imaged and counted in each sample lane. To meet quality control (QC) criteria, samples with an image binding density greater than 2.0 were reanalyzed with 2 μl of RNA. NanoString barcoding technology was previously validated for EVD gene expression (11 (link)). The RNA was hybridized with NanoString NHPV2_Immunology reporter and capture probe sets, and the RNA-probe set complexes were loaded onto an nCounter SPRINT Profiler to determine mRNA counts. This platform enables the detection of up to 769 NHP-specific immune-related transcript targets.
Woolsey C., Borisevich V., Agans K.N., Fenton K.A., Cross R.W, & Geisbert T.W. (2021). Bundibugyo ebolavirus Survival Is Associated with Early Activation of Adaptive Immunity and Reduced Myeloid-Derived Suppressor Cell Signaling. mBio, 12(4), e01517-21.
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9

Inflammatory Gene Expression Analysis by nanoString

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nanoString analysis for inflammatory genes was performed as described previously.33 , 34 (link) In brief, RNA from vehicle- or lewisite-treated skin samples was hybridized overnight at 65°C to the nanoString nCounter mouse Inflammation V2 panel (nanoString Technologies, Seattle, WA) comprising 254 genes. Hybridized samples were then immobilized onto an nCounter cartridge and imaged on an nCounter SPRINT Profiler (nanoString Technologies) as described earlier.34 (link) Data were analyzed with nSolver Analysis Software (nanoString Technologies). The threshold for significant differential expression was |1| for log2 fold change and p < 0.05 was considered for t-test significance.
Srivastava R.K., Wang Y., Khan J., Muzaffar S., Lee M.B., Weng Z., Croutch C., Agarwal A., Deshane J, & Athar M. (2022). Role of hair follicles in the pathogenesis of arsenical-induced cutaneous damage. Annals of the New York Academy of Sciences, 1515(1), 168-183.
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10

Comprehensive Profiling of Immune-Oncology Genes

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150 ng of RNA was combined with hybridization buffer and the Reporter CodeSet for the PanCancer IO 360 Panel (Nanostring) and incubated for 20 h at 65°C. The hybridized reaction was analyzed on an nCounter SPRINT Profiler (Nanostring). nSolver calculated normalization factors for each sample using raw gene counts and 14 housekeeping genes (Supplemental Table 2). Differential gene expression was calculated from normalized gene counts data and a false discovery rate with a Benjamini Hochberg multi-comparison test. The average count for the negative control probes was used for thresholding “positive” genes. After thresholding (<20 counts), a total of 666 genes were subsequently used for downstream analysis. The heatmap was generated using Clustergrammer (14 (link)). Raw gene counts are normalized using the logCPM method, filtered by selecting the genes with most variable expression, and transformed using the Z-score method.
nSolver advanced analysis tool was used to generate a pathway score for 25 different pathways (e.g., Hypoxia). The pathways scores were grouped and compared based on pre- versus post-NACT. Genetic signature analysis was performed by Nanostring and described in (15 –19 (link)). The log2-transformed gene expression values are multiplied by pre-defined weighted coefficient (16 (link)) and the sum of these values within each geneset is defined as the signature score.
Jordan K.R., Sikora M.J., Slansky J.E., Minic A., Richer J.K., Moroney M.R., Hu J., Wolsky R.J., Watson Z.L., Yamamoto T.M., Costello J.C., Clauset A., Behbakht K., Kumar T.R, & Bitler B.G. (2020). The capacity of the ovarian cancer tumor microenvironment to integrate inflammation signaling conveys a shorter disease-free interval. Clinical cancer research : an official journal of the American Association for Cancer Research, 26(23), 6362-6373.
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