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| Status |
Public on Mar 16, 2022 |
| Title |
RNA sequencing of blastocyst-stage mouse embryos in the presence or absence of RNA decay activator UPF2 |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Purpose: The goal of this study is to compare transcriptome profiles of whole blastocysts in the presence or absence of UPF2, via an approach optimized for low-input samples.
Methods: Blastocyst mRNA profiles of wild-type (WT) and Upf2 knockout (Upf2−/−) mice were generated by deep sequencing, using Illumina 2500. The sequence reads that passed quality filters were analyzed at the transcript isoform level with DESeq2 and with IsoformSwitchAnalyzeR.
Results: We identified transcripts targeted for decay by UPF2 and the NMD pathway in the blastocyst via multiple methods. We found that NMD regulates a cohort of RNAs involved in cell survival.
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| |
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| Overall design |
Blastocyst-stage embryo RNA profiling in Upf2−/− and WT mice.
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| Contributor(s) |
Chousal J |
| Citation(s) |
36255229 |
| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| R01 HD093846 |
The Role of NMD in Embryonic Development |
THE REGENTS OF THE UNIV. OF CALIF., UNIV. OF CALIF., SAN DIEGO |
MILES Frome WILKINSON |
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| |
| Submission date |
Dec 16, 2021 |
| Last update date |
Jan 06, 2023 |
| Contact name |
Heidi Cook-Andersen |
| E-mail(s) |
hcookandersen@ucsd.edu
|
| Organization name |
University of California, San Diego
|
| Department |
Department of Reproductive Medicine
|
| Street address |
2880 Torrey Pines Scenic Drive, Rm 4811
|
| City |
La Jolla |
| State/province |
California |
| ZIP/Postal code |
92037 |
| Country |
USA |
| |
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| Platforms (1) |
| GPL21103 |
Illumina HiSeq 4000 (Mus musculus) |
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| Samples (19)
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| Relations |
| BioProject |
PRJNA789489 |
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