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Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method.
The 2(-Delta Delta C(T)) method is a convenient way to analyze the relative changes in gene expression from real-time quantitative PCR experiments and two variations of the method are presented that may be useful in the analysis of real- time, quantitative PCR data.
DNA polymorphisms amplified by arbitrary primers are useful as genetic markers.
- J. Williams, A. Kubelik, K. Livak, J. Rafalski, S. Tingey
- BiologyNucleic acids research
- 25 November 1990
A new DNA polymorphism assay based on the amplification of random DNA segments with single primers of arbitrary nucleotide sequence is described, suggesting that these polymorphisms be called RAPD markers, after Random Amplified Polymorphic DNA.
Analyzing real-time PCR data by the comparative CT method
This protocol provides an overview of the comparative CT method for quantitative gene expression studies and various examples to present quantitative gene Expression data using this method.
The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells
Monocle is described, an unsupervised algorithm that increases the temporal resolution of transcriptome dynamics using single-cell RNA-Seq data collected at multiple time points that revealed switch-like changes in expression of key regulatory factors, sequential waves of gene regulation, and expression of regulators that were not known to act in differentiation.
Real-time quantification of microRNAs by stem–loop RT–PCR
A novel microRNA quantification method has been developed using stem–loop RT followed by TaqMan PCR analysis, which enables fast, accurate and sensitive miRNA expression profiling and can identify and monitor potential biomarkers specific to tissues or diseases.
Real time quantitative PCR.
Unlike other quantitative PCR methods, real-time PCR does not require post-PCR sample handling, preventing potential PCR product carry-over contamination and resulting in much faster and higher throughput assays.
Oligonucleotides with fluorescent dyes at opposite ends provide a quenched probe system useful for detecting PCR product and nucleic acid hybridization.
- K. Livak, S. Flood, J. Marmaro, W. Giusti, K. Deetz
- Biology, ChemistryPCR methods and applications
- 1 June 1995
It is proposed that the larger signal in the 5' nuclease PCR assay is caused by increased likelihood of cleavage by Taq DNA polymerase when the probe is hybridized to a template strand during PCR.
Allelic discrimination using fluorogenic probes and the 5' nuclease assay.
- K. Livak
- BiologyGenetic analysis : biomolecular engineering
- 1 February 1999
Single-cell RNA-seq supports a developmental hierarchy in human oligodendroglioma
Single-cell analyses provide insight into the cellular architecture of oligodendrogliomas at single-cell resolution and support the cancer stem cell model, with substantial implications for disease management.
Pseudo-temporal ordering of individual cells reveals dynamics and regulators of cell fate decisions
This study demonstrates that single-cell expression analysis by Monocle can uncover novel regulatory interactions governing differentiation, and reordering cells by progress through differentiation increases temporal resolution of expression measurements in a model of skeletal muscle differentiation.