Open Architecture Digital Genomics
nCounter Elements™ TagSets utilize digital, molecular barcoding chemistry based on NanoString’s patented technology that allows users to assemble their own assays. They enable counting of individual molecules with color-coded molecular barcodes via flourescent microscopy.
nCounter Elements™ TagSets may be used in conjunction with other GPRs and ASRs to create assays. Assays can be developed by simply combining nCounter Elements TagSets with unlabeled oligonucleotides that target your genes of interest. nCounter Elements enable highly multiplexed, direct profiling of individual molecules in a single reaction without amplification* and are ideal for a range of applications requiring efficient, high-precision counting of tens to hundreds of target molecules across a sample set. This unique chemistry generates high-quality results from a variety of samples types, for example: crude cell lysates or RNA purified from FFPE tissue, blood products, fine-needle aspirates or cell lines.
* Single Cell assay requires reverse transcription and amplification prior to hybridization with nCounter Elements™ TagSets.** Probes A and B are 65–85 bp oligonucleotide probes that may be purchased from an oligo supply company (not provided by NanoString).
- Digital » Digital counting of nucleic acids of interest
- Multiplexed » Multiplex up to 216 custom targets per sample in a single tube
- Simple Hybridization Workflow » 3 pipetting steps per sample; no reverse transcription, no library prep, no amplification*
- FFPE Compatible » Highly correlated when comparing Fresh Frozen and FFPE samples
- Sample Flexibility » Examples of compatible samples include: crude cell lysates or RNA/DNA purified from tissue, blood, fine-needle aspirates or cell lines.
Examples of Data Generated with nCounter Elements™ TagSets*
- Sample Types
- Single Cell
- Ordering Information
Precision Across a Large Range of Expression
The combination of digital counting with a simple, robust workflow minimizes variability. Digital counts increase linearly over a wide dynamic range facilitating accurate fold-change determination of targets of varying expression levels.
Reproducibility and Dynamic Range
Comparison of gene expression counts for 192 genes between 2 technical replicates.Replicates were hybridized with a 192-plex nCounter Elements TagSet. The data demonstrates very highly correlated counts over 4 logs of dynamic range.
Measurement Error by Expression Level (Counts)
10,000 cells were hybridized to an 192-plex nCounter Elements TagSet. Genes were grouped by level of expression and percent CV was calculated for each group. Genes expressed at less than one transcript per cell can be measured with less than 15% CV, allowing for quantitation of 2-fold changes or less even at very low levels of transcript abundance. Precision increases with expression levels, allowing for quantitation of less than 1.2-fold changes for more highly expressed genes.
Reliable Results from Challenging Sample Types
nCounter Elements enable the generation of reliable results even in challenging sample types such as Formalin-Fixed Paraffin-Embedded (FFPE) tissues or crude cell lysates. The ability to efficiently perform large studies on archival tissues and cell lines are key advantages of nCounter Elements in translational research.
FFPE and Fresh-Frozen Samples Cluster Together in Gene Expression Analysis. Twelve matched pairs of FFPE and Fresh Frozen tumor samples were analyzed with a 36-plex nCounter Elements TagSet. Each FFPE sample clusters most closely with its Fresh Frozen partner indicating that the FFPE fixation process is not confounding biological insights. Fresh Frozen datapoints were plotted against corresponding FFPE datapoints and linear regression was performed for each sample pair generating an average R2 of 0.98.
High Correlation - Purified RNA and Crude Cell Lysates
Log2 gene expression counts from 1μL crude cell lysate and 100ng purified RNA from the same sample show high correlation. Each sample was analyzed with a 192-plex nCounter Elements TagSet.
Multiplexed Target Enrichment for Ultra-Low Sample Inputs
Achieve single cell sensitivity while minimizing amplification – single tube assay provides a simple workflow & utilizes the entire sample. A Multiplexed Target Enrichment (MTE) step allows transcripts to be amplified after a reverse transcription step. MTE can amplify 216 targets from a sample in a single tube. The resulting amplified material can then be directly hybridized with nCounter Elements and target-specific probes targeting the genes of interest - no sample clean-up or sample partitioning is required.
Multiplex target enrichment enables sensitive detection of fold changes from very low sample inputs. Fold changes observed with probes using a standard nCounter Elements hybridization and input of 100ng RNA on the x-axis and 100pg prepared with MTE prior to Elements hybridization on the y-axis.