#Tophat method cellprofiler software
#Tophat method cellprofiler series

Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. TopHat: discovering splice junctions with RNA-seq. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Single-chromosome transcriptional profiling reveals chromosomal gene expression regulation. Methods of labeling cells, labeled cells, and uses thereof. Single-cell systems biology by super-resolution imaging and combinatorial labeling. The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Single-cell expression analyses during cellular reprogramming reveal an early stochastic and a late hierarchic phase.

Single-molecule mRNA decay measurements reveal promoter- regulated mRNA stability in yeast. Trcek, T., Larson, D., Moldón, A., Query, C. Stochastic mRNA synthesis in mammalian cells. Raj, A., Peskin, C.S., Tranchina, D., Vargas, D.Y. RNA sequencing reveals two major classes of gene expression levels in metazoan cells. Single-cell analysis of population context advances RNAi screening at multiple levels. CellClassifier: supervised learning of cellular phenotypes.

Rämö, P., Sacher, R., Snijder, B., Begemann, B.

#Tophat method cellprofiler series

General properties of transcriptional time series in Escherichia coli. Detection of individual endogenous RNA transcripts in situ using multiple singly labeled probes.

#Tophat method cellprofiler software

CellProfiler: image analysis software for identifying and quantifying cell phenotypes. Transcript dynamics of proinflammatory genes revealed by sequence analysis of subcellular RNA fractions. Sensitive and high-resolution detection of RNA in situ. Imaging individual mRNA molecules using multiple singly labeled probes. Raj, A., van den Bogaard, P., Rifkin, S.A., van Oudenaarden, A. Visualization of single RNA transcripts in situ. Biomarkers for differentiating melanoma from benign nevus in the skin. Detection of viral infection and gene expression in clinical tissue specimens using branched DNA (bDNA) in situ hybridization.

Single-copy gene detection using branched DNA (bDNA) in situ hybridization. Player, A.N., Shen, L.P., Kenny, D., Antao, V.P. An enhanced-sensitivity branched-DNA assay for quantification of human immunodeficiency virus type 1 RNA in plasma. Significance of serum hepatitis C virus RNA levels in chronic hepatitis C. Transcriptome sequencing of single cells with Smart-Seq. Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells. Full-length mRNA-seq from single-cell levels of RNA and individual circulating tumor cells. CEL-Seq: single-cell RNA-Seq by multiplexed linear amplification. mRNA-seq whole-transcriptome analysis of a single cell. RNA-Seq: a revolutionary tool for transcriptomics. Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution. The transcriptional landscape of the yeast genome defined by RNA sequencing. Exploring the new world of the genome with DNA microarrays. Because this method can be incorporated in a wide variety of high-throughput image-based approaches, we expect it to be broadly applicable.īrown, P.O. This has multiple implications for the functional interpretation of cell-to-cell variability in gene expression and enables the unbiased identification of functionally relevant in situ signatures of the transcriptome without the need for perturbations. In addition, it allows extraction of a multivariate feature set quantifying subcellular patterning and spatial properties of transcripts and their cell-to-cell variability. Here we show that branched DNA technology combined with automated liquid handling, high-content imaging and quantitative image analysis allows highly reproducible quantification of transcript abundance in thousands of single cells at single-molecule resolution. However, current approaches do not readily scale to the analysis of whole transcriptomes. Fluorescence in situ hybridization (FISH) is widely used to obtain information about transcript copy number and subcellular localization in single cells.