|
| Status |
Public on Sep 04, 2018 |
| Title |
Recovery and analysis of transcriptome subsets from pooled single-cell RNA-seq libraries |
| Organisms |
Homo sapiens; Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Single-cell RNA sequencing (scRNA-seq) methods generate sparse gene expression profiles for thousands of single cells in a single experiment. The information in these profiles is sufficient to classify cell types by distinct expression patterns but the high complexity of scRNA-seq libraries prevents full characterization of transcriptomes from individual cells. To generate more focused gene expression information from scRNA-seq libraries, we developed a strategy to physically recover the DNA molecules comprising transcriptome subsets, enabling deeper interrogation of the isolated molecules by another round of DNA sequencing. We applied the method in both a cell-centric and gene-centric mode to isolate mRNA fragments from scRNA-seq libraries.
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| |
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| Overall design |
targeted resequencing and original untargeted datasets of various scRNA-Seq libraries from the 10x genomics and wafergen platform
|
| |
|
| Contributor(s) |
Riemondy KA, Hesselberth JR |
| Citation(s) |
30496484 |
| Submission date |
Sep 04, 2018 |
| Last update date |
Mar 21, 2019 |
| Contact name |
Kent Augustus Riemondy |
| E-mail(s) |
kent.riemondy@cuanschutz.edu
|
| Organization name |
University of Colorado School of Medicine
|
| Department |
Biochemistry and Molecular Genetics
|
| Street address |
12801 E 17th Ave
|
| City |
Aurora |
| State/province |
Colorado |
| ZIP/Postal code |
80045 |
| Country |
USA |
| |
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| Platforms (5)
|
| GPL15520 |
Illumina MiSeq (Homo sapiens) |
| GPL20301 |
Illumina HiSeq 4000 (Homo sapiens) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
| GPL25431 |
Illumina HiSeq 4000 (Homo sapiens; Mus musculus) |
| GPL25526 |
Illumina NovaSeq 6000 (Homo sapiens; Mus musculus) |
|
| Samples (13)
|
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| Relations |
| BioProject |
PRJNA489248 |
| SRA |
SRP159524 |
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