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| Status |
Public on Jul 20, 2017 |
| Title |
Quartz-Seq2: a high-throughput single-cell RNA-sequencing method that effectively uses limited sequence reads |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
High-throughput single-cell RNA-seq methods assign limited unique molecular identifier (UMI) counts as gene expression values to single cells from shallow sequence reads and detect limited gene counts. We thus developed a high-throughput single-cell RNA-seq method, Quartz-Seq2, to overcome these issues. Our improvements in several of the reaction steps of Quartz-Seq2 allow us to effectively convert initial reads to UMI counts (at a rate of 30%–50%). To demonstrate the power of Quartz-Seq2, we analyzed transcriptomes from a cell population of in vitro embryonic stem cells and an in vivo stromal vascular fraction with a limited number of sequence reads.
Preprint: http://www.biorxiv.org/content/early/2017/07/21/159384
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| |
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| Overall design |
Technical validation of high-throughput single-cell RNA-seq methods using 10 pg total RNA. Demonstration of Quartz-Seq2 using 4,484 single-cells of embryonic stem cell and 1,052 single-cells of stromal vascular fraction (SVF).
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| Web link |
http://bit.riken.jp/
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| |
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| Contributor(s) |
Danno H, Sasagawa Y, Nikaido I |
| Citation(s) |
29523163 |
| Submission date |
Jun 09, 2017 |
| Last update date |
Jul 25, 2021 |
| Contact name |
Itoshi NIKAIDO |
| E-mail(s) |
itoshi.nikaido@riken.jp
|
| Organization name |
RIKEN
|
| Department |
Center for Biosystems Dynamics Research
|
| Lab |
Laboratory for Bioinformatics Research
|
| Street address |
2-1 Hirosawa
|
| City |
Wako |
| State/province |
Saitama |
| ZIP/Postal code |
351-0198 |
| Country |
Japan |
| |
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| Platforms (2) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
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| Samples (74)
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| Relations |
| BioProject |
PRJNA389818 |
| SRA |
SRP108899 |
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