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GEO help: Mouse over screen elements for information. |
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| Status |
Public on May 20, 2015 |
| Title |
Droplet barcoding for single cell transcriptomics applied to embryonic stem cells |
| Organisms |
Homo sapiens; Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| 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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| Overall design |
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.
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| Contributor(s) |
Klein AM, Mazutis L, Akartuna I, Tallapragada N, Veres A, Li V, Peshkin L, Weitz DA, Kirschner MW |
| Citation(s) |
26000487 |
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| Submission date |
Feb 02, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Allon M Klein |
| Organization name |
Harvard Medical School
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| Department |
Systems Biology
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| Street address |
200 Longwood Avenue
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
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| Platforms (5)
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| GPL16417 |
Illumina MiSeq (Mus musculus) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
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| Samples (8)
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| GSM1599494 |
mouse ES cells, sample 1 (935 cells) |
| GSM1599495 |
mouse ES cells, sample 2, tech Rep 1 (2.5k cells) |
| GSM1599496 |
mouse ES cells, sample 2, tech Rep 2 (3.5k cells) |
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| Relations |
| BioProject |
PRJNA274274 |
| SRA |
SRP053052 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE65525_RAW.tar |
45.0 Mb |
(http)(custom) |
TAR (of CSV) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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