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Series GSE128318 Query DataSets for GSE128318
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
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.
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.
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
Organization name Huazhong University of Science and Technology
Street address 1037
City Wuhan
ZIP/Postal code 430074
Country China
Platforms (2)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (12)
GSM3671344 CLIP1_Input_1 (RIP-Seq)
GSM3671345 CLIP1_Input_2 (RIP-Seq)
GSM3671346 CLIP1_IP_1 (RIP-Seq)
BioProject PRJNA527111
SRA SRP188449

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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
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