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| Status |
Public on May 07, 2015 |
| Title |
Multiplex Single Cell Profiling of Chromatin Accessibility by Combinatorial Cellular Indexing [RNA-seq] |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Technical advances have enabled the collection of genome and transcriptome data sets with single-cell resolution. However, single-cell characterization of the epigenome has remained challenging. Furthermore, because cells must be physically separated prior to biochemical processing, conventional single-cell preparatory methods scale linearly. We applied combinatorial cellular indexing to measure chromatin accessibility in thousands of single cells per assay, circumventing the need for compartmentalization of individual cells. We report chromatin accessibility profiles from over 15,000 single cells and use these data to cluster cells on the basis of chromatin accessibility landscapes. We identify modules of coordinately regulated chromatin accessibility at the level of single cells both between and within cell types, with a scalable method that may accelerate progress toward a human cell atlas.
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| |
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| Overall design |
3 replicates from GM12878 and HL-60 cell lines collected for differential gene expression analysis.
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| |
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| Contributor(s) |
Cusanovich DA, Daza R, Adey A, Pliner H, Christiansen L, Gunderson KL, Steemers FJ, Trapnell C, Shendure J |
| Citation(s) |
25953818 |
| |
| Submission date |
Apr 21, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Darren A. Cusanovich |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Arizona
|
| Department |
Cellular and Molecular Medicine
|
| Street address |
1230 N Cherry Avenue, BSRL 421
|
| City |
Tucson |
| State/province |
AZ |
| ZIP/Postal code |
85721 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
|
| Samples (6)
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| This SubSeries is part of SuperSeries: |
| GSE68103 |
Multiplex Single Cell Profiling of Chromatin Accessibility by Combinatorial Cellular Indexing |
|
| Relations |
| BioProject |
PRJNA281746 |
| SRA |
SRP057508 |
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