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Status |
Public on Mar 15, 2013 |
Title |
Next-generation sequencing identifies mRNAs targets that experience significant changes in alternative splicing upon PQBP1 knockdown in mouse embryonic cortical neurons |
Organism |
Mus musculus |
Experiment type |
Expression profiling by high throughput sequencing
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Summary |
PQBP1 is a highly conserved protein closely related to neurodegenerative disorders. We identified PQBP1 as an important alternative splicing effector necessary for maintaining normal neuron functions in the brain. In order to explore PQBP1's functions in alternative splicing regulation and neuronal activities, we systematically profiled the alternative splicing targets of PQBP1 in mouse embryonic cortical neurons by RNA-seq. The mRNAs whose alternative splicing are affected by PQBP1 showed tissue-specific functional enrichment especially in neurite outgrowth, with strong Gene Ontology (GO) enrichments for neuron projection development/morphogenesis, dendrite development and axonogenesis. PQBP1's alternative splicing targets are also functionally enriched in RNA splicing, chromatin modification, and ARF signal transduction.
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Overall design |
We applied RNA-seq to compare the transcriptomes of mock and PQBP1 knockdown mouse embryonic cortical neuron samples.
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Contributor(s) |
Wang Q, Silver PA |
Citation(s) |
23512658 |
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Submission date |
Feb 19, 2013 |
Last update date |
May 15, 2019 |
Contact name |
Qingqing Wang |
E-mail(s) |
qingqing_wang@berkeley.edu
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Organization name |
University of California, Berkeley
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Department |
Molecular and Cell Biology
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Lab |
Rio Lab
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Street address |
161 Koshland Hall, UC Berkeley
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City |
Berkeley |
State/province |
CA |
ZIP/Postal code |
94720 |
Country |
USA |
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Platforms (1) |
GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
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Samples (5)
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Relations |
BioProject |
PRJNA189776 |
SRA |
SRP018775 |