Transcriptomics

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Droplet barcoding for single cell transcriptomics applied to embryonic stem cells


ABSTRACT: 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. A total of 8 single cell data sets are submitted: 3 for mouse embryonic stem (ES) cells (1 biological replicate, 2 technical replicates); 3 samples following LIF withdrawal (days 2,4, 7); one pure RNA data set (from human lymphoblast K562 cells); and one sample of single K562 cells.

ORGANISM(S): Musculus  

SUBMITTER: Linas Mazutis   Naren Tallapragada  Victor Li  Allon M Klein  Adrian Veres  Ilke Akartuna  David A Weitz  Marc W Kirschner  Leonid Peshkin 

PROVIDER: E-GEOD-65525 | ArrayExpress | 2015-05-20

SECONDARY ACCESSION(S): GSE65525SRP053052PRJNA274274

REPOSITORIES: GEO, ArrayExpress, ENA

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Publications

Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells.

Klein Allon M AM   Mazutis Linas L   Akartuna Ilke I   Tallapragada Naren N   Veres Adrian A   Li Victor V   Peshkin Leonid L   Weitz David A DA   Kirschner Marc W MW  

Cell 20150501 5


It has long been the dream of biologists to map gene expression at the single-cell level. With such data one might track heterogeneous cell sub-populations, and infer regulatory relationships between genes and pathways. Recently, RNA sequencing has achieved single-cell resolution. What is limiting is an effective way to routinely isolate and process large numbers of individual cells for quantitative in-depth sequencing. We have developed a high-throughput droplet-microfluidic approach for barcod  ...[more]

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