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
81 data files
| File | Type | Size |
|---|---|---|
| HeLa_D1.fastq.gz | OTHER | 6.6 GB |
| HeLa_D2.fastq.gz | OTHER | 5.1 GB |
| HeLa_vitro_N1.fastq.gz | OTHER | 12.5 GB |
| HeLa_vitro_N2.fastq.gz | OTHER | 4.8 GB |
| HeLa_vivo_N1.fastq.gz | OTHER | 13.5 GB |
| HeLa_vivo_N2.fastq.gz | OTHER | 12.9 GB |
| HepG2_D1.fastq.gz | OTHER | 5.8 GB |
| HepG2_D2.fastq.gz | OTHER | 6.7 GB |
| HepG2_vitro_N1.fastq.gz | OTHER | 13.3 GB |
| HepG2_vitro_N2.fastq.gz | OTHER | 13.5 GB |
| HepG2_vivo_N1.fastq.gz | OTHER | 12.3 GB |
| HepG2_vivo_N2.fastq.gz | OTHER | 10.7 GB |
| K562_D1.fastq.gz | OTHER | 5.3 GB |
| K562_D2.fastq.gz | OTHER | 7.9 GB |
| K562_vitro_N1.fastq.gz | OTHER | 16.7 GB |
| K562_vitro_N2.fastq.gz | OTHER | 16.2 GB |
| K562_vivo_N1.fastq.gz | OTHER | 16.1 GB |
| K562_vivo_N2.fastq.gz | OTHER | 13.2 GB |
| MC_DMS1_Input_S48_L004_R1_001.fastq.gz | OTHER | 821.0 MB |
| MC_DMS1_IP_S49_L004_R1_001.fastq.gz | OTHER | 813.1 MB |
| MC_DMS2_Input_S50_L004_R1_001.fastq.gz | OTHER | 1017.6 MB |
| MC_DMS2_IP_S51_L004_R1_001.fastq.gz | OTHER | 932.9 MB |
| MC_NAI1_IP_S31_L007_R1_001.fastq.gz | OTHER | 1.2 GB |
| MC_NAI2_IP_S55_L008_R1_001.fastq.gz | OTHER | 1.2 GB |
| MC_noDMS1_Input_S52_L004_R1_001.fastq.gz | OTHER | 1.0 GB |
| MC_noDMS1_IP_S53_L004_R1_001.fastq.gz | OTHER | 1.0 GB |
| MC_noDMS2_Input_S54_L004_R1_001.fastq.gz | OTHER | 720.8 MB |
| MC_noDMS2_IP_S55_L004_R1_001.fastq.gz | OTHER | 811.1 MB |
| MC_noNAI1_Input_S3_L006_R1_001.fastq.gz | OTHER | 1.3 GB |
| MC_noNAI1_IP_S1_L006_R1_001.fastq.gz | OTHER | 1.5 GB |
| MC_noNAI2_Input_S4_L006_R1_001.fastq.gz | OTHER | 1.2 GB |
| MC_noNAI2_IP_S2_L006_R1_001.fastq.gz | OTHER | 937.5 MB |
| MC_vitro1_Input_S3_L002_R1_001.fastq.gz | OTHER | 1.7 GB |
| MC_vitro1_IP_S7_L002_R1_001.fastq.gz | OTHER | 897.5 MB |
| MC_vitro2_Input_S4_L002_R1_001.fastq.gz | OTHER | 1022.8 MB |
| MC_vitro2_IP_S8_L002_R1_001.fastq.gz | OTHER | 1.5 GB |
| MC_vivo1_Input_S1_L002_R1_001.fastq.gz | OTHER | 1.6 GB |
| MC_vivo1_IP_S5_L002_R1_001.fastq.gz | OTHER | 1.2 GB |
| MC_vivo2_Input_S2_L002_R1_001.fastq.gz | OTHER | 1.2 GB |
| MC_vivo2_IP_S6_L002_R1_001.fastq.gz | OTHER | 1.0 GB |
| SRR11682352_GSM4512071 | OTHER | 16.1 GB |
| SRR11682353_GSM4512072 | OTHER | 13.2 GB |
| SRR11682354_GSM4512073 | OTHER | 16.7 GB |
| SRR11682354.lite | OTHER | 16.7 GB |
| SRR11682355_GSM4512074 | OTHER | 16.2 GB |
| SRR11682356_GSM4512075 | OTHER | 12.3 GB |
| SRR11682357_GSM4512076 | OTHER | 10.7 GB |
| SRR11682358_GSM4512077 | OTHER | 13.3 GB |
| SRR11682359_GSM4512078 | OTHER | 13.5 GB |
| SRR11682360_GSM4512079 | OTHER | 13.5 GB |
| SRR11682361_GSM4512080 | OTHER | 12.9 GB |
| SRR11682362_GSM4512081 | OTHER | 12.5 GB |
| SRR11682363_GSM4512082 | OTHER | 4.8 GB |
| SRR11682364_GSM4512083 | OTHER | 1.0 GB |
| SRR11682365_GSM4512084 | OTHER | 811.0 MB |
| SRR11682366_GSM4512085 | OTHER | 1.0 GB |
| SRR11682367_GSM4512086 | OTHER | 720.0 MB |
| SRR11682368_GSM4512087 | OTHER | 813.0 MB |
| SRR11682369_GSM4512088 | OTHER | 932.0 MB |
| SRR11682370_GSM4512089 | OTHER | 821.0 MB |
| SRR11682371_GSM4512090 | OTHER | 1017.0 MB |
| SRR11682372_GSM4512091 | OTHER | 1.5 GB |
| SRR11682373_GSM4512092 | OTHER | 937.0 MB |
| SRR11682374_GSM4512093 | OTHER | 1.3 GB |
| SRR11682375_GSM4512094 | OTHER | 1.2 GB |
| SRR11682376_GSM4512095 | OTHER | 1.2 GB |
| SRR11682377_GSM4512096 | OTHER | 1.2 GB |
| SRR11682378_GSM4512097 | OTHER | 1.2 GB |
| SRR11682379_GSM4512098 | OTHER | 1.0 GB |
| SRR11682380_GSM4512099 | OTHER | 1.6 GB |
| SRR11682381_GSM4512100 | OTHER | 1.2 GB |
| SRR11682382_GSM4512101 | OTHER | 897.0 MB |
| SRR11682383_GSM4512102 | OTHER | 1.5 GB |
| SRR11682384_GSM4512103 | OTHER | 1.7 GB |
| SRR11682385_GSM4512104 | OTHER | 1022.0 MB |
| SRR12668784_GSM4795047 | OTHER | 5.3 GB |
| SRR12668785_GSM4795048 | OTHER | 7.9 GB |
| SRR12668786_GSM4795049 | OTHER | 5.8 GB |
| SRR12668787_GSM4795050 | OTHER | 6.7 GB |
| SRR12668788_GSM4795051 | OTHER | 6.6 GB |
| SRR12668789_GSM4795052 | OTHER | 5.1 GB |
Potentially related datasets 8
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 |
|---|---|---|
| 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 |
| ENCFF269URO | ENCFF · ENCODE | No title in the index |
| GSE149767 | GSE · GEO GEO ↗ | Footprinting SHAPE-eCLIP reveals transcriptome-wide hydrogen bonds at RNA-protein interfaces |
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) |