fSHAPE, fSHAPE-eCLIP, and SHAPE-eCLIP probe transcript regions that interact with specific proteins.
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).
Publication Types
["Journal Article", "Research Support, N.I.H., Extramural", "Research Support, Non-U.S. Gov't"]
MeSH Terms
["Acylation", "Blotting, Western", "Computational Biology", "Cross-Linking Reagents", "Gene Library", "Humans", "Hydrogen Bonding", "Immunoprecipitation", "K562 Cells", "Molecular Probe Techniques", "Molecular Probes", "Polymerase Chain Reaction", "Proteins", "RNA", "Ultraviolet Rays"]
Funding
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)
Linked Datasets (1)
Footprinting SHAPE-eCLIP reveals transcriptome-wide hydrogen bonds at RNA-protein interfaces
Homo sapiens160 data files
| File | Type | Size |
|---|---|---|
| HeLa_D1.fastq.gz | OTHER | 6.6 GB |
| HeLa_D1.fastq.gz | OTHER | 6.6 GB |
| HeLa_D1.fastq.gz | OTHER | 6.6 GB |
| HeLa_D1.fastq.gz | OTHER | 6.6 GB |
| HeLa_D2.fastq.gz | OTHER | 5.1 GB |
| HeLa_D2.fastq.gz | OTHER | 5.1 GB |
| HeLa_D2.fastq.gz | OTHER | 5.1 GB |
| HeLa_D2.fastq.gz | OTHER | 5.1 GB |
| HeLa_vitro_N1.fastq.gz | OTHER | 12.5 GB |
| HeLa_vitro_N1.fastq.gz | OTHER | 12.5 GB |
| HeLa_vitro_N1.fastq.gz | OTHER | 12.5 GB |
| HeLa_vitro_N1.fastq.gz | OTHER | 12.5 GB |
| HeLa_vitro_N2.fastq.gz | OTHER | 4.8 GB |
| HeLa_vitro_N2.fastq.gz | OTHER | 4.8 GB |
| HeLa_vitro_N2.fastq.gz | OTHER | 4.8 GB |
| HeLa_vitro_N2.fastq.gz | OTHER | 4.8 GB |
| HeLa_vivo_N1.fastq.gz | OTHER | 13.5 GB |
| HeLa_vivo_N1.fastq.gz | OTHER | 13.5 GB |
| HeLa_vivo_N1.fastq.gz | OTHER | 13.5 GB |
| HeLa_vivo_N1.fastq.gz | OTHER | 13.5 GB |
| HeLa_vivo_N2.fastq.gz | OTHER | 12.9 GB |
| HeLa_vivo_N2.fastq.gz | OTHER | 12.9 GB |
| HeLa_vivo_N2.fastq.gz | OTHER | 12.9 GB |
| HeLa_vivo_N2.fastq.gz | OTHER | 12.9 GB |
| HepG2_D1.fastq.gz | OTHER | 5.8 GB |
| HepG2_D1.fastq.gz | OTHER | 5.8 GB |
| HepG2_D1.fastq.gz | OTHER | 5.8 GB |
| HepG2_D1.fastq.gz | OTHER | 5.8 GB |
| HepG2_D2.fastq.gz | OTHER | 6.7 GB |
| HepG2_D2.fastq.gz | OTHER | 6.7 GB |
| HepG2_D2.fastq.gz | OTHER | 6.7 GB |
| HepG2_D2.fastq.gz | OTHER | 6.7 GB |
| HepG2_vitro_N1.fastq.gz | OTHER | 13.3 GB |
| HepG2_vitro_N1.fastq.gz | OTHER | 13.3 GB |
| HepG2_vitro_N1.fastq.gz | OTHER | 13.3 GB |
| HepG2_vitro_N1.fastq.gz | OTHER | 13.3 GB |
| HepG2_vitro_N2.fastq.gz | OTHER | 13.5 GB |
| HepG2_vitro_N2.fastq.gz | OTHER | 13.5 GB |
| HepG2_vitro_N2.fastq.gz | OTHER | 13.5 GB |
| HepG2_vitro_N2.fastq.gz | OTHER | 13.5 GB |
| HepG2_vivo_N1.fastq.gz | OTHER | 12.3 GB |
| HepG2_vivo_N1.fastq.gz | OTHER | 12.3 GB |
| HepG2_vivo_N1.fastq.gz | OTHER | 12.3 GB |
| HepG2_vivo_N1.fastq.gz | OTHER | 12.3 GB |
| HepG2_vivo_N2.fastq.gz | OTHER | 10.7 GB |
| HepG2_vivo_N2.fastq.gz | OTHER | 10.7 GB |
| HepG2_vivo_N2.fastq.gz | OTHER | 10.7 GB |
| HepG2_vivo_N2.fastq.gz | OTHER | 10.7 GB |
| K562_D1.fastq.gz | OTHER | 5.3 GB |
| K562_D1.fastq.gz | OTHER | 5.3 GB |
| K562_D1.fastq.gz | OTHER | 5.3 GB |
| K562_D1.fastq.gz | OTHER | 5.3 GB |
| K562_D2.fastq.gz | OTHER | 7.9 GB |
| K562_D2.fastq.gz | OTHER | 7.9 GB |
| K562_D2.fastq.gz | OTHER | 7.9 GB |
| K562_D2.fastq.gz | OTHER | 7.9 GB |
| K562_vitro_N1.fastq.gz | OTHER | 16.7 GB |
| K562_vitro_N1.fastq.gz | OTHER | 16.7 GB |
| K562_vitro_N2.fastq.gz | OTHER | 16.2 GB |
| K562_vitro_N2.fastq.gz | OTHER | 16.2 GB |
| K562_vitro_N2.fastq.gz | OTHER | 16.2 GB |
| K562_vitro_N2.fastq.gz | OTHER | 16.2 GB |
| K562_vivo_N1.fastq.gz | OTHER | 16.1 GB |
| K562_vivo_N1.fastq.gz | OTHER | 16.1 GB |
| K562_vivo_N1.fastq.gz | OTHER | 16.1 GB |
| K562_vivo_N1.fastq.gz | OTHER | 16.1 GB |
| K562_vivo_N2.fastq.gz | OTHER | 13.2 GB |
| K562_vivo_N2.fastq.gz | OTHER | 13.2 GB |
| K562_vivo_N2.fastq.gz | OTHER | 13.2 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_Input_S48_L004_R1_001.fastq.gz | OTHER | 821.0 MB |
| MC_DMS1_Input_S48_L004_R1_001.fastq.gz | OTHER | 821.0 MB |
| 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_DMS1_IP_S49_L004_R1_001.fastq.gz | OTHER | 813.1 MB |
| MC_DMS1_IP_S49_L004_R1_001.fastq.gz | OTHER | 813.1 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_Input_S50_L004_R1_001.fastq.gz | OTHER | 1017.6 MB |
| MC_DMS2_Input_S50_L004_R1_001.fastq.gz | OTHER | 1017.6 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_DMS2_IP_S51_L004_R1_001.fastq.gz | OTHER | 932.9 MB |
| MC_DMS2_IP_S51_L004_R1_001.fastq.gz | OTHER | 932.9 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_NAI1_IP_S31_L007_R1_001.fastq.gz | OTHER | 1.2 GB |
| MC_NAI1_IP_S31_L007_R1_001.fastq.gz | OTHER | 1.2 GB |
| 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_NAI2_IP_S55_L008_R1_001.fastq.gz | OTHER | 1.2 GB |
| MC_NAI2_IP_S55_L008_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_Input_S52_L004_R1_001.fastq.gz | OTHER | 1.0 GB |
| MC_noDMS1_Input_S52_L004_R1_001.fastq.gz | OTHER | 1.0 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_noDMS1_IP_S53_L004_R1_001.fastq.gz | OTHER | 1.0 GB |
| MC_noDMS1_IP_S53_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_Input_S54_L004_R1_001.fastq.gz | OTHER | 720.8 MB |
| MC_noDMS2_Input_S54_L004_R1_001.fastq.gz | OTHER | 720.8 MB |
| 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_noDMS2_IP_S55_L004_R1_001.fastq.gz | OTHER | 811.1 MB |
| MC_noDMS2_IP_S55_L004_R1_001.fastq.gz | OTHER | 811.1 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_Input_S3_L006_R1_001.fastq.gz | OTHER | 1.3 GB |
| MC_noNAI1_Input_S3_L006_R1_001.fastq.gz | OTHER | 1.3 GB |
| 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_noNAI1_IP_S1_L006_R1_001.fastq.gz | OTHER | 1.5 GB |
| MC_noNAI1_IP_S1_L006_R1_001.fastq.gz | OTHER | 1.5 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_Input_S4_L006_R1_001.fastq.gz | OTHER | 1.2 GB |
| MC_noNAI2_Input_S4_L006_R1_001.fastq.gz | OTHER | 1.2 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_noNAI2_IP_S2_L006_R1_001.fastq.gz | OTHER | 937.5 MB |
| MC_noNAI2_IP_S2_L006_R1_001.fastq.gz | OTHER | 937.5 MB |
| 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_Input_S3_L002_R1_001.fastq.gz | OTHER | 1.7 GB |
| MC_vitro1_Input_S3_L002_R1_001.fastq.gz | OTHER | 1.7 GB |
| 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_vitro1_IP_S7_L002_R1_001.fastq.gz | OTHER | 897.5 MB |
| MC_vitro1_IP_S7_L002_R1_001.fastq.gz | OTHER | 897.5 MB |
| 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_Input_S4_L002_R1_001.fastq.gz | OTHER | 1022.8 MB |
| MC_vitro2_Input_S4_L002_R1_001.fastq.gz | OTHER | 1022.8 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_vitro2_IP_S8_L002_R1_001.fastq.gz | OTHER | 1.5 GB |
| MC_vitro2_IP_S8_L002_R1_001.fastq.gz | OTHER | 1.5 GB |
| 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_Input_S1_L002_R1_001.fastq.gz | OTHER | 1.6 GB |
| MC_vivo1_Input_S1_L002_R1_001.fastq.gz | OTHER | 1.6 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_vivo1_IP_S5_L002_R1_001.fastq.gz | OTHER | 1.2 GB |
| MC_vivo1_IP_S5_L002_R1_001.fastq.gz | OTHER | 1.2 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_Input_S2_L002_R1_001.fastq.gz | OTHER | 1.2 GB |
| MC_vivo2_Input_S2_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 |
| MC_vivo2_IP_S6_L002_R1_001.fastq.gz | OTHER | 1.0 GB |
| MC_vivo2_IP_S6_L002_R1_001.fastq.gz | OTHER | 1.0 GB |
| MC_vivo2_IP_S6_L002_R1_001.fastq.gz | OTHER | 1.0 GB |
| SRR11682354.lite | OTHER | 16.7 GB |
| SRR11682354.lite | OTHER | 16.7 GB |
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