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| Status |
Public on Sep 21, 2019 |
| Title |
Transcriptome-wide analysis of wild-type and SRSF3-knockout glioma stem-like cells |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Purpose: The splicing factor SRSF3 is a member of serine- and arginine-rich proteins, which is frequently upregulated in various types of cancer. The aim of this study is to profile the alternative splicing (AS) events that were regulated by SRSF3 in glioma stem-like cells (GSCs).
Methods: Total RNAs isolated from GSC83 and GSC528 cells with SRSF3-konckout (KO) or control (WT) were subjected to paired-end RNA-seq using the Illumina NextSeq 500 system according to the manufacturer's instruction. Raw reads were subjected to quality control and then aligned with HISAT2 to the human genome hg19. Quantification was performed using HTSeq-count. Differential expression of genes was calculated by DESeq2. For the splicing analysis, the mapped reads were processed through the MISO pipeline to estimate expression of alternatively spliced isoforms. The PSI (Percent Spliced In) values were calculated for each annotated AS event.
Results: We identified a total of 2752 and 2548 SRSF3-regulated AS events in GSC83 and 528 cells, respectively, with 1143 events shared by these two GSC cell lines.
Conclusions: Our study defines SRSF3 as a master regulator of glioma-associated AS program, implicating SRSF3 as an oncogenic factor for tumorigenesis and a potential therapeutic target for GBM treatment.
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| Overall design |
Transcriptome profiles of GSC83-WT, GSC83-SRSF3-KO, GSC528-WT, and GSC528-SRSF3-KO were generated by next generation sequencing, using Illumina NextSeq 500 system.
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| Contributor(s) |
Song X, Zeng C, Zhang W, Cheng S |
| Citation(s) |
31462429 |
| |
| Submission date |
Apr 30, 2019 |
| Last update date |
Sep 23, 2019 |
| Contact name |
Xiao Song |
| E-mail(s) |
xiao.song@northwestern.edu
|
| Phone |
3122738044
|
| Organization name |
Northwestern University Feinberg School of Medicine
|
| Department |
Neurology
|
| Lab |
Shiyuan Cheng
|
| Street address |
303 E Superior St, Lurie 6-250
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60611 |
| Country |
USA |
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| Platforms (1) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
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| Samples (4)
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| Relations |
| BioProject |
PRJNA540487 |
| SRA |
SRP194266 |
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