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| Status |
Public on Nov 01, 2019 |
| Title |
An ultra high-throughput method for single-cell joint analysis of open chromatin and transcriptome |
| Organisms |
Homo sapiens; Mus musculus |
| Experiment type |
Other
|
| Summary |
Simultaneous profiling of transcriptome and chromatin accessibility within single cells is a powerful approach to dissect gene regulatory programs in complex tissues. However, the current tools are limited by modest throughput. We now describe an ultra high-throughput method, Paired-seq, for parallel analysis of transcriptome and accessible chromatin in millions of single cells. We demonstrate the utility of Paired-seq for analyzing the dynamic and cell-type specific gene regulatory programs in complex tissues, by applying it to mouse adult cerebral cortex and fetal forebrain. The joint profiles of a large number of single cells allowed us to deconvolute the transcriptome and open chromatin landscapes in the major cell types within these brain tissues, infer putative target genes of candidate enhancers, and reconstruct the trajectory of cellular lineages within the developing forebrain.
*** For cell-gene/bin-counts matrix of fetal forebrain and adult cerebral cortex, please download from: http://renlab.sdsc.edu/chz272/Paired_seq_sorted_matrices/
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| |
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| Overall design |
Combined analysis of RNA and accessible chromatin in single-cells.
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| |
|
| Contributor(s) |
Zhu C, Yu M, Ren B |
| Citation(s) |
31695190 |
| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| U54 HG006997 |
Center for Mammalian Regulatory Genomics |
Ludwig Institute for Cancer Research Ltd |
Bing Ren |
|
| Submission date |
Apr 26, 2019 |
| Last update date |
Apr 27, 2020 |
| Contact name |
Zhu Chenxu |
| E-mail(s) |
cxzhu@pku.edu.cn, czhu@nygenome.org
|
| Organization name |
New York Genome Center
|
| Street address |
101 Avenue of the Americas
|
| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10044 |
| Country |
USA |
| |
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| Platforms (3) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
| GPL21103 |
Illumina HiSeq 4000 (Mus musculus) |
| GPL22245 |
Illumina HiSeq 2500 (Homo sapiens; Mus musculus) |
|
| Samples (16)
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| Relations |
| BioProject |
PRJNA539985 |
| SRA |
SRP194005 |
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