Direct multiplexed measurement of gene expression with color-coded probe pairs

By G. Geiss, Roger E Bumgarner, Brian Birditt, Timothy Dahl, N. Dowidar, D. Dunaway, H. Fell, S. Ferree, Renee D George, Tammy Grogan and 11 more. Nature Biotechnology, 2008

2,064 citations recorded by the source corpus.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/9f481a34e910e3ee3f56bdcd23b089b0bb7d7d60

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Molecular Biology

Citations in the corpus

Improving RNA-Seq expression estimates by correcting for fragment bias (2011, critical): “We examined the recently published NanoString nCounter gene expression system [14], but noticed many unexplainable out-liers and high variance between technical replicates (see Figure S4 of Additional file 1 and data in Additional file 2).”
Peroxisomes are signaling platforms for antiviral innate immunity (2010, result): “We confirmed these results by examining the expression of several candidate IFNs and ISGs using nCounter, which allows for multiplex analysis of gene expression with the sensitivity of quantitative RT-PCR (Geiss et al., 2008) (Figures S4A and S4B).”
RNA sequencing: advances, challenges and opportunities (2010, methodology): “The probe mixture is hybridized to RNA samples in solution, followed by the immobilization of probe–RNA duplexes on surfaces and single-molecule imaging to identify and count individual transcript”
Revisiting Global Gene Expression Analysis (2012, neutral): “Global gene expression analysis uses DNA microarrays, RNA-Seq, and other methods to measure the levels of RNA species in biological systems (Geiss et al., 2008; Heller, 2002; Lockhart and Winzeler, 2000; Ozsolak and Milos, 2011; Schena et al., 1998; Wang et al., 2009).”
Annotating non-coding regions of the genome (2010, background): “On the experimental side, new medium-throughput techniques are under development to increase the number of predictions that can be validated (for example, the NanoString nCounte”
Systems medicine: the future of medical genomics and healthcare (2009, methodology): “use miniaturized high-throughput reverse-transcriptase PCR [55] or multiplex direct visualization and counting of RNA molecules; the latter technology has the added advantage of avoiding biases resulting from reverse transcription [56].”
Noninvasive prenatal diagnosis of fetal chromosomal aneuploidy by massively parallel genomic sequencing of DNA in maternal plasma (2008, background): “In fact, other non-sequencing-based methods of single-molecule analyses may be suitable for our application and may ultimately prove to be more cost effective (28).”
Membrane-Bound IL-21 Promotes Sustained Ex Vivo Proliferation of Human Natural Killer Cells (2012, methodology): “After the last wash cells were resuspended in PBS containing 0.1% BSA, 10 mg/ml RNAse A (Cayman Chemical) and 0.06 mg/ml propidium iodide (BD Biosciences), incubated 2–3 h at room temperature and analyzed on a FACSCalibur flow cytometer (BD Biosciences).”
Genomic positional conservation identifies topological anchor point (tap)RNAs linked to developmental loci (2016, methodology): “…these results and extend to a larger and more diverse set of human and mouse tissues and cell types, we used the Nanostring expression assay, which provides a versatile platform for parallel single molecule detection of targeted RNAs with high sensitivity and specificity (Geiss et al., 2008).”
CRISPR-Cas9 Knockin Mice for Genome Editing and Cancer Modeling (2014, methodology): “5% of the lysate was hybridized for 16 hr with a previously described Nanostring Gene Expression CodeSet (Geiss et al., 2008) and loaded into the nCounter Prep Station followed by quantification using the nCounter Digital Analyzer.”