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| Status |
Public on Jun 24, 2015 |
| Title |
Single cell RNA-seq data of human hESCs to evaluate Oscope - a statistical pipeline for identifying oscillatory genes in unsynchronized single cell RNA-Seq |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Oscillatory gene expression is fundamental to mammalian development, but technologies to monitor expression oscillations are limited. We have developed a statistical approach called Oscope to identify and characterize the transcriptional dynamics of oscillating genes in single-cell RNA-seq data from an unsynchronized cell population. Applications to a number of data sets, include a single-cell RNA-seq data set of human embroyonic stem cells (hESCs), demonstrate advantages of the approach and also identify a potential artifact in the Fluidigm C1 platform.
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| Overall design |
Total 213 H1 single cells and 247 H1-Fucci single cells were sequenced. The 213 H1 cells were used to evaluate Oscope in identifying oscillatory genes. The H1-Fucci cells were used to confirm the cell cycle gene cluster identified by Oscope in the H1 hESCs. Normalized expected counts are provided in GSE64016_H1andFUCCI_normalized_EC.csv.gz
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| Contributor(s) |
Ning L, Li-Fang C |
| Citation(s) |
26301841 |
| |
| Submission date |
Dec 09, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Ning Leng |
| E-mail(s) |
lengning1@gmail.com
|
| Organization name |
Morgridge Institute for Research
|
| Street address |
330 N Orchard St
|
| City |
Madison |
| State/province |
WI |
| ZIP/Postal code |
53715 |
| Country |
USA |
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| Platforms (1) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
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| Samples (460)
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| Relations |
| BioProject |
PRJNA269761 |
| SRA |
SRP050992 |
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