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| Status |
Public on Sep 23, 2019 |
| Title |
Transcriptome-wide identification of splicing defects upon XAB2 knockdown |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
We performed RNA-seq to determine the impact of XAB2 depletion on global splicing. The results show that XAB2 depletion using two different siRNAs led to a wide range of splicing defects, with more than 50% events were intron retention.
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| Overall design |
HeLa cells were transfected with control or XAB2 siRNA for 48 h. Total RNA was then purified using TRIzol, treated with DNase I and Ribo-Zero rRNA Removal kit to generate sequencing libraries, and subjected to strand-specific paired-end RNA-seq analyses using Illumina Hiseq X Ten platform by Novogene company (China). We used junction usage model (JUM) program to identify XAB2-regulated differential alternative pre-mRNA splicing events.
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| Contributor(s) |
Hou S, Lei H |
| Citation(s) |
31216022 |
| Submission date |
Apr 19, 2019 |
| Last update date |
Sep 23, 2019 |
| Contact name |
Shuai Hou |
| E-mail(s) |
houshuai@dmu.edu.cn
|
| Organization name |
Dalian Medical University
|
| Department |
cancer stem cell institute
|
| Street address |
lvshun south road no.9
|
| City |
Dalian |
| State/province |
Liaoning |
| ZIP/Postal code |
116044 |
| Country |
China |
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| Platforms (1) |
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| Samples (6)
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| Relations |
| BioProject |
PRJNA533814 |
| SRA |
SRP193107 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE130087_siX_1_vs_NC_JUM_AS_differential_A3SS_events_pvalue_0.05_final_simplified.txt.gz |
266.4 Kb |
(ftp)(http) |
TXT |
| GSE130087_siX_1_vs_NC_JUM_AS_differential_A5SS_events_pvalue_0.05_final_simplified.txt.gz |
100.3 Kb |
(ftp)(http) |
TXT |
| GSE130087_siX_1_vs_NC_JUM_AS_differential_MXE_events_pvalue_0.05_final_simplified.txt.gz |
313 b |
(ftp)(http) |
TXT |
| GSE130087_siX_1_vs_NC_JUM_AS_differential_cassette_exon_events_pvalue_0.05_final_simplified.txt.gz |
179.8 Kb |
(ftp)(http) |
TXT |
| GSE130087_siX_1_vs_NC_JUM_AS_differential_composite_events_pvalue_0.05_final_simplified.txt.gz |
525.6 Kb |
(ftp)(http) |
TXT |
| GSE130087_siX_1_vs_NC_JUM_AS_differential_intron_retention_pvalue_0.05_final_simplified.txt.gz |
677.0 Kb |
(ftp)(http) |
TXT |
| GSE130087_siX_2_vs_NC_JUM_AS_differential_A3SS_events_pvalue_0.05_final_simplified.txt.gz |
227.4 Kb |
(ftp)(http) |
TXT |
| GSE130087_siX_2_vs_NC_JUM_AS_differential_A5SS_events_pvalue_0.05_final_simplified.txt.gz |
88.0 Kb |
(ftp)(http) |
TXT |
| GSE130087_siX_2_vs_NC_JUM_AS_differential_MXE_events_pvalue_0.05_final_simplified.txt.gz |
558 b |
(ftp)(http) |
TXT |
| GSE130087_siX_2_vs_NC_JUM_AS_differential_cassette_exon_events_pvalue_0.05_final_simplified.txt.gz |
154.4 Kb |
(ftp)(http) |
TXT |
| GSE130087_siX_2_vs_NC_JUM_AS_differential_composite_events_pvalue_0.05_final_simplified.txt.gz |
397.3 Kb |
(ftp)(http) |
TXT |
| GSE130087_siX_2_vs_NC_JUM_AS_differential_intron_retention_pvalue_0.05_final_simplified.txt.gz |
614.6 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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