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| Status |
Public on Jun 16, 2015 |
| Title |
Single-cell RNA-Seq transcriptome analysis of circular RNAs in mouse embryos |
| Organisms |
Homo sapiens; Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
We reported a new method of single-cell universal poly(A)-independent RNA sequencing (SUPeR-seq) to obtain single cell whole transcriptome analysis that covers both poly(A) plus and poly(A) minus RNA species. We built libraries of single mouse ESC , 10pg, 100pg and 1ng diluted mouse ES total RNA, single HEK293T cell and mouse early embryos before 4-cell stage. We analyzed these data using bioinformatics and find a good coverage of non-polyadenylated RNAs, circular RNA for example. to make a comparison,we also used mouse ES cells and HEK293T cells to build libraries using the protocol publish by F.Tang in 2009(sample name Tang2009_*). We also de novo assembled new genes in mouse ESCs and early embryo samples, further validated known and novel zygotic genes with a-Aminatine treated 2-cell embryos(sample name SUPeR-seq_a-AM_treated_2-cell*).
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| Overall design |
3 Single mouse ES cells, 7 single HEK293T cells, 8 diluted mouse ES total RNA samples and 19 mouse embryo samples are performed using SUPeR-seq to evaluate its ability to detect genes in single RNAs and to cover poly(A)- RNA species.
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| Contributor(s) |
Fan X, Zhang X |
| Citation(s) |
26201400 |
| Submission date |
Dec 17, 2013 |
| Last update date |
Nov 06, 2019 |
| Contact name |
Xiaoying Fan |
| E-mail(s) |
sharryfan100@gmail.com
|
| Organization name |
Peking University
|
| Department |
College of Life Sciences
|
| Lab |
Biodynamic Optical Imaging Center
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| Street address |
5 Yiheyuan Road
|
| City |
Beijing |
| State/province |
Beijing |
| ZIP/Postal code |
100871 |
| Country |
China |
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| Platforms (4)
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| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
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| Samples (118)
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| Relations |
| BioProject |
PRJNA231896 |
| SRA |
SRP034543 |
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