fSHAPE, fSHAPE-eCLIP, and SHAPE-eCLIP probe transcript regions that interact with specific proteins.
Meredith Corley, Ryan A Flynn, Steven M Blue, Brian A Yee, Howard Y Chang, Gene W Yeo
STAR protocols · 2021 · Vol. 2 (3) · pp. 100762
Abstract
Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) structure probing techniques characterize the secondary structure of RNA molecules, which influence their functions and interactions. A variation of SHAPE, footprinting SHAPE (fSHAPE), probes RNA in the presence and absence of protein to identify RNA bases that hydrogen-bond with protein. SHAPE or fSHAPE coupled with enhanced crosslinking and immunoprecipitation (SHAPE-eCLIP or fSHAPE-eCLIP) pulls down RNAs bound by any protein of interest and returns their structure or protein interaction information, respectively. Here, we describe detailed protocols for SHAPE-eCLIP and fSHAPE-eCLIP and an analysis protocol for fSHAPE. For complete details on the use and execution of these protocols, please refer to Corley et al. (2020).
Linked datasets 1
Footprinting SHAPE-eCLIP reveals transcriptome-wide hydrogen bonds at RNA-protein interfaces
Homo sapiens
10 data files
| File | Type | Size |
|---|---|---|
| HeLa_D1.fastq.gz | OTHER | 6.6 GB |
| HeLa_D2.fastq.gz | OTHER | 5.1 GB |
| HepG2_D1.fastq.gz | OTHER | 5.8 GB |
| HepG2_D2.fastq.gz | OTHER | 6.7 GB |
| K562_D1.fastq.gz | OTHER | 5.3 GB |
| K562_D2.fastq.gz | OTHER | 7.9 GB |
| K562_vivo_N1.fastq.gz | OTHER | 16.1 GB |
| K562_vivo_N2.fastq.gz | OTHER | 13.2 GB |
| MC_vitro1_Input_S3_L002_R1_001.fastq.gz | OTHER | 1.7 GB |
| MC_vitro2_Input_S4_L002_R1_001.fastq.gz | OTHER | 1022.8 MB |
Potentially related datasets 7
These accessions were text-mined from the PMC full text. They may be referenced for comparison, cited from other studies, or otherwise mentioned without being primary data for this paper.
| Accession | Source | Title |
|---|---|---|
| ENCFF269URO | ENCFF · ENCODE | No title in the index |
| SRR11682379 | SRR · SRA | No title in the index |
| SRR11682385 | SRR · SRA | No title in the index |
| SRR11682378 | SRR · SRA | No title in the index |
| SRR11682382 | SRR · SRA | No title in the index |
| SRR11682383 | SRR · SRA | No title in the index |
| SRR11682384 | SRR · SRA | No title in the index |
Funding 7 grants
| Grant | Funder |
|---|---|
| R01 HG004659 | NHGRI NIH HHS (United States) |
| U41 HG009889 | NHGRI NIH HHS (United States) |
| R01 HL137223 | NHLBI NIH HHS (United States) |
| R01 HL137219 | NHLBI NIH HHS (United States) |
| T32 CA009302 | NCI NIH HHS (United States) |
| R35 CA209919 | NCI NIH HHS (United States) |
| R01 HD085902 | NICHD NIH HHS (United States) |