Tuesday, 21 September 2010

Whole transcriptome of a single cell using NGS

I think the holy grail of gene profiling has to be single molecule sequencing from a single cell. Imagine the amount of de novo transcriptomics projects that will spring up when that becomes an eventuality!
Posted by Alison Leon on Aug 12, 2010 2:00:42 PM
Are you struggling with conducting gene expression analysis from limited sample amounts? Or perhaps you're trying to keep up with new developments in stem cell research. If so, you might be interested in a recent Cell Stem Cell publication discussing single-cell RNA-Seq analysis (Tang et al., Cell Stem Cell, 2010). In their research, Tang and colleagues trace the conversion of mouse embryonic stem cells from the inner cell mass (ICM) to pluripotent embryonic stem cells (ESCs), revealing molecular changes in the process. This is a follow-on to two previous papers, in which the proof of concept (Tang et al., Nature Methods, 2009) and protocols (Tang et al., Nature Protocols, 2010) for these experiments were detailed.

Using the SOLiD™ System (16-plex, 50-base reads) and whole transcriptome software tools, researchers performed whole transcriptome analysis at the single-cell level (an unprecedented resolution!) to determine gene expression levels and identify novel splice junctions. 385 genes in 74 individual cells were monitored during their transition from ICM to ESC. Validation with TaqMan® assays corroborated this method’s high sensitivity and reproducibility.

According to Tang et al., this research could form the basis for future studies involving regulation and differentiation of stem cells in adults. In addition, further knowledge about developing stem cells could lead to information about how disease tissues, including cancers, develop.

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