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| Status |
Public on Sep 16, 2020 |
| Title |
Transcriptome-wide maps of STRAP-RNA interactions in mouse early embryo and lineage-committed cells. |
| Organism |
Mus musculus |
| Experiment type |
Other
|
| Summary |
We report the application of enhanced cross-linking immunoprecipitation (eCLIP) sequencing technology for high-throughput profiling of STRAP-RNA interactions in mouse embryos (E9.5) or embryoid body (EB) cells. Based on the eCLIP-seq data, we computationally identified a transcriptome-wide set of high-confidence peaks (over ten thousands) and most of STRAP-peaks distributed in the murine genome by defining certain exons and introns as well as their intersection. STRAP eCLIP signals in embryos were dramatically enriched at exon/intron and intron/exon borders. Numerous STRAP peaks are significantly enriched on the genes with critical roles in early organ development. Finally, we show two examples of STRAP-RNA binding that link to its regulated genes at the alternative splicing level. Together, we uncover the position- and context- dependent effects of STRAP on splicing regulation during mouse embryonic stem cells lineage commitment. Our studies provide a very useful platform to decipher STRAP’s role in the many steps in RNA biogenesis for future studies.
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| |
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| Overall design |
Examination of STRAP-RNA interactions in mouse embryos and embryoid body cells.
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| |
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| Contributor(s) |
Datta PK, Jin L |
| Citation(s) |
33230114 |
| |
| Submission date |
May 20, 2019 |
| Last update date |
Dec 08, 2020 |
| Contact name |
Pran K Datta |
| E-mail(s) |
prandatta@uabmc.edu
|
| Phone |
2059756039
|
| Organization name |
University of Alabama at Birmingham
|
| Department |
Medicine
|
| Lab |
WTI 530
|
| Street address |
1824 6th Ave South, WTI 520C
|
| City |
Birmingham |
| State/province |
AL |
| ZIP/Postal code |
35294 |
| Country |
USA |
| |
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| Platforms (1) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
|
| Samples (6)
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| This SubSeries is part of SuperSeries: |
| GSE131474 |
STRAP-dependent alternative splicing events; STRAP-RNA interactions in mouse early embryo and lineage-committed cells. |
|
| Relations |
| BioProject |
PRJNA543791 |
| SRA |
SRP198922 |
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