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| Status |
Public on Sep 16, 2020 |
| Title |
Next generation sequencing facilitates quantitative analysis of STRAP-dependent alternative splicing events |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
We report the application of next generation sequencing for evaluating alternative splicing (AS) events on lineage-committed WT and Strap-KO embryoid body (EB) cells. We also analyzed AS during mouse embryo development using RNA-seq data. Of all STRAP-regulated AS, exon-skipping events were the most frequent ones with significant changes in 49% (240 out of 489) cases. Retained introns were also overrepresented (20%, 97 out of 489) as compared to other types of AS STRAP appears to function in promoting both exon inclusion and skipping at different exons. GO function revealed STRAP-regulated AS events involve in protein catabolism, molecular binding and cell motility. More specifically, they included neuronal migration and development. Together, these analyses uncovered the previous unknown role of STRAP involved in the substantial transcriptional diversity at the exon level in certain development stage. Our study also represents the first detailed analysis of AS events in the mouse early organogenesis with biologic replicates, generated by RNA-seq technology.
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| |
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| Overall design |
Examination of STRAP- and development-regulated AS events, respectively.
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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 |
| |
|
| Platforms (1) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
|
| Samples (10)
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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 |
PRJNA543790 |
| SRA |
SRP198923 |
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