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Series GSE19323 Query DataSets for GSE19323
Status Public on Dec 24, 2009
Title PTB CLIP-seq
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Recent transcriptome analysis indicates that >90% of human genes undergoes alternative splicing, underscoring the contribution of differential RNA processing to diverse proteomes in higher eukaryotic cells. The polypyrimidine tract binding protein PTB is a well-characterized splicing repressor, but PTB knockdown causes both exon inclusion and skipping. Genome-wide mapping of PTB-RNA interactions and construction of a functional RNA map now revealed that dominant PTB binding near a competing constitutive splice site generally induces exon inclusion whereas prevalent binding close to an alternative site often causes exon skipping. This positional effect was further demonstrated by disrupting or creating a PTB binding site on minigene constructs and testing their responses to PTB knockdown or overexpression. These findings suggest a mechanism for PTB to modulate splice site competition to produce opposite functional consequences, which may be generally applicable to RNA binding splicing factors to positively or negatively regulate alternative splicing in mammalian cells.
Overall design Examination of PTB-RNA binding in Hela cells using CLIP-seq (Cross-Linking ImmunoPrecipitation coupled with high-throughput sequencing) method.

Peaks: The four alignment files (linked as supplementary files on Sample records) were combined together for peak finding, as we found that most of the monomeric and dimeric tags are similarly distributed in the genome with high pearson correlation coefficient. The method to detect the peaks above gene-specific randomized background was similar to (Yeo et al., 2009) and described in the paper (Xue et al., 2009).
Contributor(s) Xue Y, Zhou Y, Wu T, Zhu T, Ji X, Kwon Y, Zhang C, Yeo G, Black DL, Sun H, Fu X, Zhang Y
Citation(s) 20064465
Submission date Dec 04, 2009
Last update date May 15, 2019
Contact name Xiang-Dong Fu
Organization name UC San Diego
Department CMM
Lab George Palade Laboratories
Street address 9500 Gilman Drive, Room 231
City La Jolla
State/province CA
ZIP/Postal code 92093-0651
Country USA
Platforms (1)
GPL9052 Illumina Genome Analyzer (Homo sapiens)
Samples (4)
GSM480476 Human_PTB_CLIP-seq_M1
GSM480477 Human_PTB_CLIP-seq_M2
GSM480478 Human_PTB_CLIP-seq_D1
SRA SRP001758
BioProject PRJNA120867

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE19323_RAW.tar 52.8 Mb (http)(custom) TAR (of BED)
GSE19323_ptb_peak_cluster.bed.gz 555.0 Kb (ftp)(http) BED
SRA Run SelectorHelp
Processed data provided as supplementary file
Processed data are available on Series record
Raw data are available in SRA

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