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Droplet barcoding for single cell transcriptomics applied to embryonic stem cells

GSE65525 Homo sapiens; Mus musculus Expression profiling by high throughput sequencing 8 samples Submitted 2015/05/20 Platform GPL16417Platform GPL17021Platform GPL18573Platform GPL19057Platform GPL16791
Summary
Recently, RNA sequencing has achieved single cell resolution, but what is limiting is an effective way to routinely isolate and process large numbers of individual cells for in-depth sequencing, and to do so quantitatively. We have developed a droplet-microfluidic approach for parallel barcoding thousands of individual cells for subsequent RNA profiling by next-generation sequencing. This high-throughput method shows a surprisingly low noise profile and is readily adaptable to other sequencing-based assays. Using this technique, we analyzed mouse embryonic stem cells, revealing in detail the population structure and the heterogeneous onset of differentiation after LIF withdrawal. The reproducibility and low noise of this high-throughput single cell data allowed us to deconstruct cell populations and infer gene expression relationships.
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Direct links to NCBI, no account and no request form: the whole study as GSE65525_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 8 samples. Raw sequencing reads are also available from ENA.

Also filed as BioProject PRJNA274274 and SRA study SRP053052. Searching any of these in the dataset finder brings you back here.

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