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| Status |
Public on Feb 07, 2022 |
| Title |
Transcriptome-wide identification of RNA binding protein binding sites using seCLIP-seq |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Discovery of interaction sites between RNA-binding proteins (RBPs) and their RNA targets plays a critical role in enabling our understanding of how these RBPs control RNA processing and regulation. Cross-linking and immunoprecipitation (CLIP) provides a generalizable, transcriptome-wide method by which RBP:RNA complexes are purified and sequenced to identify sites of intermolecular contact. By simplifying technical challenges in prior CLIP methods and incorporating the generation of and quantitative comparison against size-matched input controls, the single-end enhanced CLIP (seCLIP) protocol allows for the profiling of these interactions with high resolution, efficiency, and scalability.
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| Overall design |
Identification of PRPF39 targets using transcriptome-wide seCLIP-seq in HepG2 cells.
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| Contributor(s) |
Blue SM, Yee BA, Pratt GA, Meuller JR, Park SS, Van Nostrand EL, Yeo EW |
| Citation(s) |
35322209 |
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| Submission date |
Jul 23, 2021 |
| Last update date |
May 09, 2022 |
| Contact name |
Gene Yeo |
| E-mail(s) |
[email protected]
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| Organization name |
UCSD
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| Street address |
2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab
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| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92037 |
| Country |
USA |
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| Platforms (1) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (4)
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| Relations |
| BioProject |
PRJNA749175 |
| SRA |
SRP329582 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE180686_4114_CLIP1_rep1.vs.4114_CLIP2_rep2.bed.gz |
143.5 Kb |
(ftp)(http) |
BED |
| GSE180686_RAW.tar |
178.7 Mb |
(http)(custom) |
TAR (of BED, BW) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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