Islam2011 Data: Characterization of the single-cell transcriptional landscape by highly multiplex RNA-Seq

By (Secondary Ownership. The experiment uses only third-party data.)

This is an independent re-analysis of the data published by Islam et al.
In this analysis, we have processed and aligned all datasets and from this stage onward focused only on datasets with a certain minimum coverage -- medium = at least 250,000 aligned reads or high = at least 500,000 aligned reads.

Description from GEO:

Summary Our understanding of the development and maintenance of tissues has been greatly aided by large-scale gene expression analysis. However, tissues are invariably complex, and expression analysis of a tissue confounds the true expression patterns of its constitutent cell types. Here we describe a novel strategy to access such complex samples. Single-cell RNA-Seq expression profiles were generated, and clustered to form a two-dimensional cell map onto which expression data was projected. The resulting cell map integrates three levels of organization: the whole population of cells, the functionally distinct subpopulations it contains, and the single cells themselves -- all without need for known markers to classify cell types. The feasibility of the strategy was demonstrated by analyzing the complete transcriptomes of 92 single cells of two distinct types. We believe this strategy will enable the unbiased discovery and analysis of naturally occurring cell types during development, adult physiology and disease.

Overall design 92 single cells (48 mouse ES cells, 44 mouse embryonic fibroblasts and 4 negative controls) were analyzed by single-cell tagged reverse transcription (STRT)
RNA-seq single-cell stem cells gene expression / transcription
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Illumina Genome Analyzer II
SRP006834

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Input Data

Sample Groups and Experimental Factors


Genome Snapshots

'Genome snapshots' are assorted genomic regions that the creators of this experiment considered of particular interest.

Nanog Locus, Single Cell RNA-seq

Pou5f1 Locus, Single Cell RNA-seq

Lin28 Locus, Single Cell RNA-seq

Main Experimental Results

This is a selection of main results from the data analysis in this experiment. All intermediate results and more data are available from the workflow designer.

Other data generated in this experiment:

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Analysis Workflow

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