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| Status |
Public on Aug 29, 2018 |
| Title |
Joint profiling of chromatin accessibility and gene expression in thousands of single cells |
| Organisms |
Homo sapiens; Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Here we describe sci-CAR, a combinatorial indexing strategy to jointly profile chromatin accessibility and mRNA in each of thousands of single cells. As a proof-of-concept, we apply sci-CAR to 4,825 cells comprising a time-series of dexamethasone treatment, as well as to 11,233 cells from the mouse kidney.
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| Overall design |
single cell RNA-seq and ATAC-seq co-profiling for HEK293T cells, NIH/3T3 cells, A549 cells across three treatment conditions (DEX 0 hour, 1 hour and 3 hour treatment), and wild type mouse kidney.
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| Contributor(s) |
Cao J, Cusanovich DA, Ramani V, Pliner H, Hill A, Aghamirzaie D, Daza RM, McFaline J, Packer JS, Christiansen L, Steemers FJ, Adey A, Trapnell C, Shendure J |
| Citation(s) |
30166440 |
| Submission date |
Jul 13, 2018 |
| Last update date |
Mar 25, 2019 |
| Contact name |
Junyue Cao |
| E-mail(s) |
cao1025@uw.edu
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| Organization name |
University of Washington
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| Department |
Department of Genome Sciences
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| Lab |
Shendure lab
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| Street address |
Foege Building S-210, 3720 15th Ave NE
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| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98195-5065 |
| Country |
USA |
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| Platforms (2) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
| GPL19415 |
Illumina NextSeq 500 (Homo sapiens; Mus musculus) |
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| Samples (6)
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| GSM3271040 |
HEK293T, NIH/3T3, A549 cells, sci-CAR RNA-seq |
| GSM3271041 |
HEK293T, NIH/3T3, A549 cells, sci-CAR ATAC-seq |
| GSM3271042 |
HEK293T, NIH/3T3, A549 cells, sci-RNA-seq |
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| Relations |
| BioProject |
PRJNA481032 |
| SRA |
SRP153396 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE117089_RAW.tar |
232.2 Mb |
(http)(custom) |
TAR (of CSV, TXT) |
| GSE117089_README.txt |
5.5 Kb |
(ftp)(http) |
TXT |
| GSE117089_README_filenames_to_SRR.txt |
113.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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