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| Status |
Public on Dec 15, 2021 |
| Title |
CLIP1 and DMD are two novel RNA-binding proteins through computational prediction and experimental validation |
| Organism |
Homo sapiens |
| Experiment type |
Other
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| Summary |
Since RBPs play important roles in the cell, it’s particularly important to find new RBPs. We performed iRIP-seq and CLIP-seq to verify two proteins, CLIP1 and DMD, predicted by RBPPred whether are RBPs or not. The experimental results confirm that these two proteins have RNA-binding activity. We identified significantly enriched binding motifs UGGGGAGG, CUUCCG and CCCGU for CLIP1 (iRIP-seq), DMD (iRIP-seq) and DMD (CLIP-seq), respectively. The computational KEGG and GO analysis show that the CLIP1 and DMD share some biological processes and functions. Besides, we found that the SNPs between DMD and its RNA partners may associate with Becker muscular dystrophy, Duchenne muscular dystrophy, Dilated cardiomyopathy 3B and Cardiovascular phenotype. Among the thirteen cancers data, CLIP1 and another 300 genes always co-occur, and 123 of these 300 genes interact with CLIP1. These cancers may be associated with the mutations in both CLIP1 and the genes it interacts with.
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| Overall design |
iRIP-seq and CLIP-seq was performed in biological replicate for CLIP1 and DMD in HeLa cell. Each sample has a input control for analysis.
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| Contributor(s) |
Xie J, Zhang X, Zheng J, Hong X, Tong X, Liu X, Xue Y, Wang X, Zhang Y, Liu S |
| Citation(s) |
34921931 |
| Submission date |
Mar 14, 2019 |
| Last update date |
Jan 04, 2022 |
| Contact name |
Shiyong Liu |
| E-mail(s) |
liushiyong@gmail.com
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| Organization name |
Huazhong University of Science and Technology
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| Street address |
1037
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| City |
Wuhan |
| ZIP/Postal code |
430074 |
| Country |
China |
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| Platforms (2) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (12)
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| Relations |
| BioProject |
PRJNA527111 |
| SRA |
SRP188449 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE128318_bedfiles_CLIP-Seq.tar.gz |
1.1 Mb |
(ftp)(http) |
TAR |
| GSE128318_bedfiles_iRIP-Seq.tar.gz |
4.9 Mb |
(ftp)(http) |
TAR |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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