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| Status |
Public on Feb 14, 2020 |
| Title |
Oocytes, a single cell and a tissue |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Development of single cell sequencing allows detailing the transcriptome of individual oocytes. Here, we compare different RNA-seq datasets from single and pooled mouse oocytes and show higher reproducibility using single oocyte RNA-seq. We further demonstrate that UMI (unique molecular identifiers) based and other deduplication methods are limited in their ability to improve the precision of these datasets. Finally, for normalization of sample differences in cross-stage comparisons, we propose that external spike-in molecules are comparable to using the endogenous genes stably expressed during oocyte maturation. The ability to normalize data among single cells provides insight into the heterogeneity of mouse oocytes.
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| Overall design |
To confirm the ERCC normalization, we performed mouse single oocyte RNA-seq with different amplification cycles during library preparation and also different fractions of GV oocytes (1/2, 1/4, 1/8).
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| Contributor(s) |
Wu D, Jurrien D |
| Citation(s) |
35321242 |
| |
| Submission date |
Feb 13, 2020 |
| Last update date |
Mar 31, 2022 |
| Contact name |
Di Wu |
| E-mail(s) |
[email protected]
|
| Organization name |
HHMI Janelia
|
| Department |
4DCP
|
| Street address |
19700 Helix Drive
|
| City |
Ashburn |
| State/province |
Virginia |
| ZIP/Postal code |
20147 |
| Country |
USA |
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| Platforms (1) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
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| Samples (12)
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| Relations |
| BioProject |
PRJNA606592 |
| SRA |
SRP249380 |
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