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Series GSE44402 Query DataSets for GSE44402
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
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.
Overall design We applied RNA-seq to compare the transcriptomes of mock and PQBP1 knockdown mouse embryonic cortical neuron samples.
Contributor(s) Wang Q, Silver PA
Citation(s) 23512658
Submission date Feb 19, 2013
Last update date May 15, 2019
Contact name Qingqing Wang
Organization name University of California, Berkeley
Department Molecular and Cell Biology
Lab Rio Lab
Street address 161 Koshland Hall, UC Berkeley
City Berkeley
State/province CA
ZIP/Postal code 94720
Country USA
Platforms (1)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (5)
GSM1084565 mock_knockdown_rep1
GSM1084566 mock_knockdown_rep2
GSM1084567 mock_knockdown_rep3
BioProject PRJNA189776
SRA SRP018775

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Supplementary file Size Download File type/resource
GSE44402_QW_Table_S2-AS_targets_of_PQBP1_identified_from_RNA-seq.xlsx.gz 139.4 Kb (ftp)(http) XLSX
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