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GSE149767

GSE GEO
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Footprinting SHAPE-eCLIP reveals transcriptome-wide hydrogen bonds at RNA-protein interfaces

Organism: Homo sapiens
Platform: GPL11154
Samples: 40
Experiment Types:
Other Third-party reanalysis
Submitted: May 03 2020
Last Updated: Sep 08 2021
Status: Public on Nov 30 2020
Contact: Gene,,Yeo (UCSD)

Relations

Reanalysis of: GSM2075716 Reanalysis of: GSM2075717 Reanalysis of: GSM2075718 Reanalysis of: GSM2075719 Reanalysis of: GSM2075714 Reanalysis of: GSM2075715 BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA630074 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP259971

Summary

Discovering the interaction mechanism and location of RNA binding proteins (RBPs) on RNA is critical for understanding gene expression regulation. Here, we apply selective 2’-hydroxyl acylation analyzed by primer extension (SHAPE) on in vivo transcripts to identify transcriptome-wide footprints (fSHAPE) on RNA when compared to protein-absent transcripts. Structural analyses indicate that fSHAPE precisely detects nucleotides whose base moieties hydrogen bond with protein and that fSHAPE patterns can predict binding sites of RBPs of interest. To illustrate, we demonstrate that fSHAPE correctly identifies known and novel iron response protein RNA elements. Furthermore, we enable selective interrogation of RNA-protein complexes by integrating SHAPE and fSHAPE with crosslinking and immunoprecipitation (eCLIP) of desired RBPs. To demonstrate, histone stem loop elements and their nucleotides that hydrogen bond with stem-loop binding protein were identified by SHAPE-eCLIP and fSHAPE-eCLIP. Together, these technologies greatly expand on strategies for understanding specific cellular RNA interactions in RNA-protein complexes.

Overall Design

Footprinting and SHAPE structure probing of human cells was performed in conjunction with enhanced crosslinking and immunoprecipitation in order to interrogate cellular RNA-protein complexes in a targeted manner. fSHAPE was performed on multiple human cell lines and identifies hydrogen bonds that occur between RNA base moieties and interacting protein residues. fSHAPE-eCLIP was performed on K562 cells with immunoprecipitation for stem loop binding protein (SLBP) and both identifies SLBP transcript binding sites as well as bases that hydrogen bond with protein. SHAPE-eCLIP was performed on K562 cells with immunoprecipitation for SLBP and identifies SLBP transcript binding sites as well as returning RNA structure probing information in these sites. in vivo click (ic)SHAPE structure probing, performed in parallel with fSHAPE, produces base pairing probailities (i.e. "reactivities") at each nucleotide across transcripts. Please note that [1] each processed data was generated from multiple samples/replicates as indicated in the corresponding sample description field. [2] the 293T_vitro_icSHAPE.tar.gz files were generated from re-analyzing the samples GSM2075714-GSM2075717. The 293T_vivo_icSHAPE.tar.gz files were generated from re-analyzing the samples GSM2075714-GSM2075715, GSM2075718-GSM2075719 (in GSE74353; third-party re-analysis). [3] the 293tmaps.tar.gz files were generated from re-analyzing the samples GSM2075716-GSM2075719 (in GSE74353; third-party re-analysis).

Analysis (14 steps)

View Data Processing
Processing steps for GSE149767
  1. library strategy: footprinting and selective 2’-hydroxyl acylation analyzed by primer extension (fSHAPE)
  2. SHAPE libraries as follows:
  3. Full code at https://github.com/meracorley/fSHAPE
  4. zcat "$file".fastq.gz | umi_tools extract --bc-pattern=NNNNCCCCNNNNN > "$file".umi.fastq
  5. cutadapt -a AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG --minimum-length=23 --overlap=5 -o "$file".trim.fastq "$file".umi.fastq
  6. STAR --runThreadN 8 --genomeDir /projects/ps-yeolab4/genomes/GRCh38/star/ --readFilesIn "$file".trim.fastq --outFileNamePrefix "$file" --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --outSAMtype BAM SortedByCoordinate
  7. umitools dedup -I "$file"Aligned.sortedByCoord.out.bam --spliced-is-unique -S "$file".dedup.bam
  8. Total coverage (bedtools genomecov -split -strand + -dz; bedtools genomecov -split -strand - -dz) and 5' end coverage (bedtools genomecov -5 -strand + -dz; bedtools genomecov -5 -strand - -dz) summed at each position in the transcriptome with de-duplicated reads.
Showing first 8 steps.

Supplementary Files (20)

GSE149767_293t_vitro_icshape.tar.gz Download
GSE149767_293t_vivo_icshape.tar.gz Download
GSE149767_293tmaps.tar.gz Download
GSE149767_dms_shapeclip_maps.tar.gz Download
GSE149767_fshape_clip_maps.tar.gz Download
GSE149767_hela_vitro_icshape.tar.gz Download
GSE149767_hela_vivo_icshape.tar.gz Download
GSE149767_helamaps.tar.gz Download
GSE149767_hepg2_vitro_icshape.tar.gz Download
GSE149767_hepg2_vivo_icshape.tar.gz Download
GSE149767_hepg2maps.tar.gz Download
GSE149767_k562_vitro_icshape.tar.gz Download
GSE149767_k562_vivo_icshape.tar.gz Download
GSE149767_k562maps.tar.gz Download
GSE149767_nai_shapeclip_maps.tar.gz Download
GSE149767_nodms_reproducible_peaks.hg38.bed.gz Download
GSE149767_nonai_reproducible_peaks.hg38.bed.gz Download
GSE149767_readme.txt Download
GSE149767_vitro_reproducible_peaks.hg38.bed.gz Download
GSE149767_vivo_reproducible_peaks.hg38.bed.gz Download
GEO Samples (40)
GSM4512071 GSM4512072 GSM4512073 GSM4512074 GSM4512075 GSM4512076 GSM4512077 GSM4512078 GSM4512079 GSM4512080 GSM4512081 GSM4512082 GSM4512083 GSM4512084 GSM4512085 GSM4512086 GSM4512087 GSM4512088 GSM4512089 GSM4512090 GSM4512091 GSM4512092 GSM4512093 GSM4512094 GSM4512095 GSM4512096 GSM4512097 GSM4512098 GSM4512099 GSM4512100 GSM4512101 GSM4512102 GSM4512103 GSM4512104 GSM4795047 GSM4795048 GSM4795049 GSM4795050 GSM4795051 GSM4795052

Dataset Citations (2)

Footprinting SHAPE-eCLIP Reveals Transcriptome-wide Hydrogen Bonds at RNA-Protein Interfaces.
PMID 33242392 · 2020 · Molecular cell
Meredith Corley, Ryan A Flynn, Byron Lee, Steven M Blue, Howard Y Chang, Gene W Yeo
fSHAPE, fSHAPE-eCLIP, and SHAPE-eCLIP probe transcript regions that interact with specific proteins.
PMID 34485935 · 2021 · STAR protocols
Meredith Corley, Ryan A Flynn, Steven M Blue, Brian A Yee, Howard Y Chang, Gene W Yeo

SRA Experiments (40) and Runs (40)

Total: 222929 MB
SRX8243208 SRP259971 OTHER SINGLE
GSM4512073: K562 fSHAPE vitro rep1; Homo sapiens; OTHER
Sample: SRS6591844
BioProject: PRJNA630074
BioSample: SAMN14823585
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: K562 fSHAPE vitro
cell line: K562
rna probing reagent: NAI-N3
rna state when probed: in vitro
Original files (1)
K562 fSHAPE vitro
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR11682354 539421996 37881519033 17107.55 K562_vitro_N1.fastq.gz, SRR11682354, SRR11682354.lite SRA
SRX8243209 SRP259971 OTHER SINGLE
GSM4512074: K562 fSHAPE vitro rep2; Homo sapiens; OTHER
Sample: SRS6591845
BioProject: PRJNA630074
BioSample: SAMN14823584
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: K562 fSHAPE vitro
cell line: K562
rna probing reagent: NAI-N3
rna state when probed: in vitro
Original files (1)
K562 fSHAPE vitro
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR11682355 510759060 36538174190 16631.09 K562_vitro_N2.fastq.gz, SRR11682355, SRR11682355.lite SRA
SRX8243210 SRP259971 OTHER SINGLE
GSM4512075: HepG2 fSHAPE vivo rep1; Homo sapiens; OTHER
Sample: SRS6591846
BioProject: PRJNA630074
BioSample: SAMN14823583
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: HepG2 fSHAPE vivo
cell line: HepG2
rna probing reagent: NAI-N3
rna state when probed: in vivo
Original files (1)
HepG2 fSHAPE vivo
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR11682356 378445538 28350477865 12546.89 HepG2_vivo_N1.fastq.gz, SRR11682356, SRR11682356.lite SRA
SRX8243211 SRP259971 OTHER SINGLE
GSM4512076: HepG2 fSHAPE vivo rep2; Homo sapiens; OTHER
Sample: SRS6591847
BioProject: PRJNA630074
BioSample: SAMN14823582
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: HepG2 fSHAPE vivo
cell line: HepG2
rna probing reagent: NAI-N3
rna state when probed: in vivo
Original files (1)
HepG2 fSHAPE vivo
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR11682357 322405674 24170041940 10954.03 HepG2_vivo_N2.fastq.gz, SRR11682357, SRR11682357.lite SRA
SRX8243212 SRP259971 OTHER SINGLE
GSM4512077: HepG2 fSHAPE vitro rep1; Homo sapiens; OTHER
Sample: SRS6591848
BioProject: PRJNA630074
BioSample: SAMN14823581
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: HepG2 fSHAPE vitro
cell line: HepG2
rna probing reagent: NAI-N3
rna state when probed: in vitro
Original files (1)
HepG2 fSHAPE vitro
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR11682358 411405111 31106699437 13643.85 HepG2_vitro_N1.fastq.gz, SRR11682358, SRR11682358.lite SRA
SRX8243213 SRP259971 OTHER SINGLE
GSM4512078: HepG2 fSHAPE vitro rep2; Homo sapiens; OTHER
Sample: SRS6591849
BioProject: PRJNA630074
BioSample: SAMN14823580
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: HepG2 fSHAPE vitro
cell line: HepG2
rna probing reagent: NAI-N3
rna state when probed: in vitro
Original files (1)
HepG2 fSHAPE vitro
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR11682359 420334044 31795525793 13859.79 HepG2_vitro_N2.fastq.gz, SRR11682359, SRR11682359.lite SRA
SRX8243214 SRP259971 OTHER SINGLE
GSM4512079: HeLa fSHAPE vivo rep1; Homo sapiens; OTHER
Sample: SRS6591850
BioProject: PRJNA630074
BioSample: SAMN14823579
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: HeLa fSHAPE vivo
cell line: HeLa
rna probing reagent: NAI-N3
rna state when probed: in vivo
Original files (1)
HeLa fSHAPE vivo
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR11682360 411207176 30275270194 13838.99 HeLa_vivo_N1.fastq.gz, SRR11682360, SRR11682360.lite SRA
SRX8243215 SRP259971 OTHER SINGLE
GSM4512080: HeLa fSHAPE vivo rep2; Homo sapiens; OTHER
Sample: SRS6591851
BioProject: PRJNA630074
BioSample: SAMN14823578
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: HeLa fSHAPE vivo
cell line: HeLa
rna probing reagent: NAI-N3
rna state when probed: in vivo
Original files (1)
HeLa fSHAPE vivo
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR11682361 393323128 29022844242 13198.82 HeLa_vivo_N2.fastq.gz, SRR11682361, SRR11682361.lite SRA
SRX8243216 SRP259971 OTHER SINGLE
GSM4512081: HeLa fSHAPE vitro rep1; Homo sapiens; OTHER
Sample: SRS6591852
BioProject: PRJNA630074
BioSample: SAMN14823577
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: HeLa fSHAPE vitro
cell line: HeLa
rna probing reagent: NAI-N3
rna state when probed: in vitro
Original files (1)
HeLa fSHAPE vitro
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR11682362 387193895 28099180797 12761.62 HeLa_vitro_N1.fastq.gz, SRR11682362, SRR11682362.lite SRA
SRX8243217 SRP259971 OTHER SINGLE
GSM4512082: HeLa fSHAPE vitro rep2; Homo sapiens; OTHER
Sample: SRS6591853
BioProject: PRJNA630074
BioSample: SAMN14823576
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: HeLa fSHAPE vitro
cell line: HeLa
rna probing reagent: NAI-N3
rna state when probed: in vitro
Original files (1)
HeLa fSHAPE vitro
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR11682363 146105156 10715504276 4890.56 HeLa_vitro_N2.fastq.gz, SRR11682363, SRR11682363.lite SRA
SRX8243218 SRP259971 OTHER SINGLE
GSM4512083: SHAPE-eCLIP noDMS IP rep1; Homo sapiens; OTHER
Sample: SRS6591854
BioProject: PRJNA630074
BioSample: SAMN14823575
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: SHAPE-eCLIP noDMS IP
cell line: K562
rna probing reagent: None
rna state when probed: in vivo
eclip antibody: SLBP (MBLI RN045P Lot#001)
Original files (1)
SHAPE-eCLIP noDMS IP
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR11682364 38568871 2892665325 1049.14 MC_noDMS1_IP_S53_L004_R1_001.fastq.gz, SRR11682364, SRR11682364.lite SRA
SRX8243219 SRP259971 OTHER SINGLE
GSM4512084: SHAPE-eCLIP noDMS IP rep2; Homo sapiens; OTHER
Sample: SRS6591855
BioProject: PRJNA630074
BioSample: SAMN14823574
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: SHAPE-eCLIP noDMS IP
cell line: K562
rna probing reagent: None
rna state when probed: in vivo
eclip antibody: SLBP (MBLI RN045P Lot#001)
Original files (1)
SHAPE-eCLIP noDMS IP
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR11682365 30095262 2257144650 811.08 MC_noDMS2_IP_S55_L004_R1_001.fastq.gz, SRR11682365, SRR11682365.lite SRA
SRX8243220 SRP259971 OTHER SINGLE
GSM4512085: SHAPE-eCLIP noDMS Input rep1; Homo sapiens; OTHER
Sample: SRS6591856
BioProject: PRJNA630074
BioSample: SAMN14823573
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: SHAPE-eCLIP noDMS Input
cell line: K562
rna probing reagent: None
rna state when probed: in vivo
eclip antibody: None
Original files (1)
SHAPE-eCLIP noDMS Input
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR11682366 38555986 2891698950 1030.69 MC_noDMS1_Input_S52_L004_R1_001.fastq.gz, SRR11682366, SRR11682366.li… SRA
SRX8243221 SRP259971 OTHER SINGLE
GSM4512086: SHAPE-eCLIP noDMS Input rep2; Homo sapiens; OTHER
Sample: SRS6591857
BioProject: PRJNA630074
BioSample: SAMN14823572
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: SHAPE-eCLIP noDMS Input
cell line: K562
rna probing reagent: None
rna state when probed: in vivo
eclip antibody: None
Original files (1)
SHAPE-eCLIP noDMS Input
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR11682367 26737919 2005343925 720.76 MC_noDMS2_Input_S54_L004_R1_001.fastq.gz, SRR11682367, SRR11682367.li… SRA
SRX8243222 SRP259971 OTHER SINGLE
GSM4512087: SHAPE-eCLIP DMS IP rep1; Homo sapiens; OTHER
Sample: SRS6591858
BioProject: PRJNA630074
BioSample: SAMN14823571
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: SHAPE-eCLIP DMS IP
cell line: K562
rna probing reagent: dimethyl sulfate (DMS)
rna state when probed: in vivo
eclip antibody: SLBP (MBLI RN045P Lot#001)
Original files (1)
SHAPE-eCLIP DMS IP
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR11682368 30407101 2280532575 813.07 MC_DMS1_IP_S49_L004_R1_001.fastq.gz, SRR11682368, SRR11682368.lite SRA
SRX8243223 SRP259971 OTHER SINGLE
GSM4512088: SHAPE-eCLIP DMS IP rep2; Homo sapiens; OTHER
Sample: SRS6591859
BioProject: PRJNA630074
BioSample: SAMN14823604
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: SHAPE-eCLIP DMS IP
cell line: K562
rna probing reagent: dimethyl sulfate (DMS)
rna state when probed: in vivo
eclip antibody: None
Original files (1)
SHAPE-eCLIP DMS IP
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR11682369 34343130 2575734750 932.93 MC_DMS2_IP_S51_L004_R1_001.fastq.gz, SRR11682369, SRR11682369.lite SRA
SRX8243224 SRP259971 OTHER SINGLE
GSM4512089: SHAPE-eCLIP DMS Input rep1; Homo sapiens; OTHER
Sample: SRS6591860
BioProject: PRJNA630074
BioSample: SAMN14823603
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: SHAPE-eCLIP DMS Input
cell line: K562
rna probing reagent: dimethyl sulfate (DMS)
rna state when probed: in vivo
eclip antibody: None
Original files (1)
SHAPE-eCLIP DMS Input
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR11682370 30795061 2309629575 821.04 MC_DMS1_Input_S48_L004_R1_001.fastq.gz, SRR11682370, SRR11682370.lite SRA
SRX8243225 SRP259971 OTHER SINGLE
GSM4512090: SHAPE-eCLIP DMS Input rep2; Homo sapiens; OTHER
Sample: SRS6591861
BioProject: PRJNA630074
BioSample: SAMN14823602
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: SHAPE-eCLIP DMS Input
cell line: K562
rna probing reagent: dimethyl sulfate (DMS)
rna state when probed: in vivo
eclip antibody: SLBP (MBLI RN045P Lot#001)
Original files (1)
SHAPE-eCLIP DMS Input
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR11682371 37925632 2844422400 1017.57 MC_DMS2_Input_S50_L004_R1_001.fastq.gz, SRR11682371, SRR11682371.lite SRA
SRX8243226 SRP259971 OTHER SINGLE
GSM4512091: SHAPE-eCLIP noNAI IP rep1; Homo sapiens; OTHER
Sample: SRS6591862
BioProject: PRJNA630074
BioSample: SAMN14823601
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: SHAPE-eCLIP noNAI IP
cell line: K562
rna probing reagent: None
rna state when probed: in vivo
eclip antibody: SLBP (MBLI RN045P Lot#001)
Original files (1)
SHAPE-eCLIP noNAI IP
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR11682372 52184984 3931514096 1487.51 MC_noNAI1_IP_S1_L006_R1_001.fastq.gz, SRR11682372, SRR11682372.lite SRA
SRX8243227 SRP259971 OTHER SINGLE
GSM4512092: SHAPE-eCLIP noNAI IP rep2; Homo sapiens; OTHER
Sample: SRS6591863
BioProject: PRJNA630074
BioSample: SAMN14823600
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: SHAPE-eCLIP noNAI IP
cell line: K562
rna probing reagent: None
rna state when probed: in vivo
eclip antibody: SLBP (MBLI RN045P Lot#001)
Original files (1)
SHAPE-eCLIP noNAI IP
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR11682373 32544849 2450006161 937.46 MC_noNAI2_IP_S2_L006_R1_001.fastq.gz, SRR11682373, SRR11682373.lite SRA
SRX8243228 SRP259971 OTHER SINGLE
GSM4512093: SHAPE-eCLIP noNAI Input rep1; Homo sapiens; OTHER
Sample: SRS6591864
BioProject: PRJNA630074
BioSample: SAMN14823599
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: SHAPE-eCLIP noNAI Input
cell line: K562
rna probing reagent: None
rna state when probed: in vivo
eclip antibody: None
Original files (1)
SHAPE-eCLIP noNAI Input
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR11682374 45938293 3461805477 1309.63 MC_noNAI1_Input_S3_L006_R1_001.fastq.gz, SRR11682374, SRR11682374.lite SRA
SRX8243229 SRP259971 OTHER SINGLE
GSM4512094: SHAPE-eCLIP noNAI Input rep2; Homo sapiens; OTHER
Sample: SRS6591865
BioProject: PRJNA630074
BioSample: SAMN14823598
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: SHAPE-eCLIP noNAI Input
cell line: K562
rna probing reagent: None
rna state when probed: in vivo
eclip antibody: None
Original files (1)
SHAPE-eCLIP noNAI Input
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR11682375 44386482 3345591825 1265.13 MC_noNAI2_Input_S4_L006_R1_001.fastq.gz, SRR11682375, SRR11682375.lite SRA
SRX8243230 SRP259971 OTHER SINGLE
GSM4512095: SHAPE-eCLIP NAI IP rep1; Homo sapiens; OTHER
Sample: SRS6591867
BioProject: PRJNA630074
BioSample: SAMN14823597
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: SHAPE-eCLIP NAI IP
cell line: K562
rna probing reagent: 2-methylnicotinic acid imidazolide (NAI)
rna state when probed: in vivo
eclip antibody: SLBP (MBLI RN045P Lot#001)
Original files (1)
SHAPE-eCLIP NAI IP
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR11682376 41923378 3160996285 1188.05 MC_NAI1_IP_S31_L007_R1_001.fastq.gz, SRR11682376, SRR11682376.lite SRA
SRX8243231 SRP259971 OTHER SINGLE
GSM4512096: SHAPE-eCLIP NAI IP rep2; Homo sapiens; OTHER
Sample: SRS6591866
BioProject: PRJNA630074
BioSample: SAMN14823596
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: SHAPE-eCLIP NAI IP
cell line: K562
rna probing reagent: 2-methylnicotinic acid imidazolide (NAI)
rna state when probed: in vivo
eclip antibody: SLBP (MBLI RN045P Lot#001)
Original files (1)
SHAPE-eCLIP NAI IP
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR11682377 44378624 3348936023 1240.97 MC_NAI2_IP_S55_L008_R1_001.fastq.gz, SRR11682377, SRR11682377.lite SRA
SRX8243232 SRP259971 OTHER SINGLE
GSM4512097: fSHAPE-eCLIP vivo IP rep1; Homo sapiens; OTHER
Sample: SRS6591868
BioProject: PRJNA630074
BioSample: SAMN14823595
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: fSHAPE-eCLIP vivo IP
cell line: K562
rna probing reagent: 2-methylnicotinic acid imidazolide (NAI)
rna state when probed: in vivo
eclip antibody: SLBP (MBLI RN045P Lot#001)
Original files (1)
fSHAPE-eCLIP vivo IP
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR11682378 45010174 3420773224 1276.97 MC_vivo1_IP_S5_L002_R1_001.fastq.gz, SRR11682378, SRR11682378.lite SRA
SRX8243233 SRP259971 OTHER SINGLE
GSM4512098: fSHAPE-eCLIP vivo IP rep2; Homo sapiens; OTHER
Sample: SRS6591869
BioProject: PRJNA630074
BioSample: SAMN14823594
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: fSHAPE-eCLIP vivo IP
cell line: K562
rna probing reagent: 2-methylnicotinic acid imidazolide (NAI)
rna state when probed: in vivo
eclip antibody: SLBP (MBLI RN045P Lot#001)
Original files (1)
fSHAPE-eCLIP vivo IP
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR11682379 35686037 2712138812 1032.17 MC_vivo2_IP_S6_L002_R1_001.fastq.gz, SRR11682379, SRR11682379.lite SRA
SRX8243234 SRP259971 OTHER SINGLE
GSM4512099: fSHAPE-eCLIP vivo Input rep1; Homo sapiens; OTHER
Sample: SRS6591870
BioProject: PRJNA630074
BioSample: SAMN14823593
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: fSHAPE-eCLIP vivo Input
cell line: K562
rna probing reagent: 2-methylnicotinic acid imidazolide (NAI)
rna state when probed: in vivo
eclip antibody: None
Original files (1)
fSHAPE-eCLIP vivo Input
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR11682380 55731971 4235629796 1607.46 MC_vivo1_Input_S1_L002_R1_001.fastq.gz, SRR11682380, SRR11682380.lite SRA
SRX8243235 SRP259971 OTHER SINGLE
GSM4512100: fSHAPE-eCLIP vivo Input rep2; Homo sapiens; OTHER
Sample: SRS6591872
BioProject: PRJNA630074
BioSample: SAMN14823592
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: fSHAPE-eCLIP vivo Input
cell line: K562
rna probing reagent: 2-methylnicotinic acid imidazolide (NAI)
rna state when probed: in vivo
eclip antibody: None
Original files (1)
fSHAPE-eCLIP vivo Input
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR11682381 42206569 3207699244 1224.13 MC_vivo2_Input_S2_L002_R1_001.fastq.gz, SRR11682381, SRR11682381.lite SRA
SRX8243236 SRP259971 OTHER SINGLE
GSM4512101: fSHAPE-eCLIP vitro IP rep1; Homo sapiens; OTHER
Sample: SRS6591871
BioProject: PRJNA630074
BioSample: SAMN14823591
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: fSHAPE-eCLIP vitro IP
cell line: K562
rna probing reagent: 2-methylnicotinic acid imidazolide (NAI)
rna state when probed: in vitro
eclip antibody: SLBP (MBLI RN045P Lot#001)
Original files (1)
fSHAPE-eCLIP vitro IP
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR11682382 31244720 2374598720 897.46 MC_vitro1_IP_S7_L002_R1_001.fastq.gz, SRR11682382, SRR11682382.lite SRA
SRX8243237 SRP259971 OTHER SINGLE
GSM4512102: fSHAPE-eCLIP vitro IP rep2; Homo sapiens; OTHER
Sample: SRS6591873
BioProject: PRJNA630074
BioSample: SAMN14823590
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: fSHAPE-eCLIP vitro IP
cell line: K562
rna probing reagent: 2-methylnicotinic acid imidazolide (NAI)
rna state when probed: in vitro
eclip antibody: SLBP (MBLI RN045P Lot#001)
Original files (1)
fSHAPE-eCLIP vitro IP
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR11682383 52501213 3990092188 1533.12 MC_vitro2_IP_S8_L002_R1_001.fastq.gz, SRR11682383, SRR11682383.lite SRA
SRX8243238 SRP259971 OTHER SINGLE
GSM4512103: fSHAPE-eCLIP vitro Input rep1; Homo sapiens; OTHER
Sample: SRS6591874
BioProject: PRJNA630074
BioSample: SAMN14823589
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: fSHAPE-eCLIP vitro Input
cell line: K562
rna probing reagent: 2-methylnicotinic acid imidazolide (NAI)
rna state when probed: in vitro
eclip antibody: None
Original files (1)
fSHAPE-eCLIP vitro Input
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR11682384 61944485 4707780860 1774.78 MC_vitro1_Input_S3_L002_R1_001.fastq.gz, SRR11682384, SRR11682384.lite SRA
SRX8243239 SRP259971 OTHER SINGLE
GSM4512104: fSHAPE-eCLIP vitro Input rep2; Homo sapiens; OTHER
Sample: SRS6591876
BioProject: PRJNA630074
BioSample: SAMN14823588
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: fSHAPE-eCLIP vitro Input
cell line: K562
rna probing reagent: 2-methylnicotinic acid imidazolide (NAI)
rna state when probed: in vitro
eclip antibody: None
Original files (1)
fSHAPE-eCLIP vitro Input
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR11682385 35069498 2665281848 1022.78 MC_vitro2_Input_S4_L002_R1_001.fastq.gz, SRR11682385, SRR11682385.lite SRA
SRX8243240 SRP259971 OTHER SINGLE
GSM4512071: K562 fSHAPE vivo rep1; Homo sapiens; OTHER
Sample: SRS6591875
BioProject: PRJNA630074
BioSample: SAMN14823587
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: K562 fSHAPE vivo
cell line: K562
rna probing reagent: NAI-N3
rna state when probed: in vivo
Original files (1)
K562 fSHAPE vivo
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR11682352 501036946 35894961440 16514.45 K562_vivo_N1.fastq.gz, SRR11682352, SRR11682352.lite SRA
SRX8243241 SRP259971 OTHER SINGLE
GSM4512072: K562 fSHAPE vivo rep2; Homo sapiens; OTHER
Sample: SRS6591877
BioProject: PRJNA630074
BioSample: SAMN14823586
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: K562 fSHAPE vivo
cell line: K562
rna probing reagent: NAI-N3
rna state when probed: in vivo
Original files (1)
K562 fSHAPE vivo
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR11682353 424425669 30213139152 13546.03 K562_vivo_N2.fastq.gz, SRR11682353, SRR11682353.lite SRA
SRX9149333 SRP259971 OTHER SINGLE
GSM4795047: K562 untreated rep1; Homo sapiens; OTHER
Sample: SRS7390125
BioProject: PRJNA630074
BioSample: SAMN16205938
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: K562 untreated
cell line: K562
rna probing reagent: None
Original files (1)
K562 untreated
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR12668784 169246638 12118941083 5460.53 K562_D1.fastq.gz, SRR12668784, SRR12668784.lite SRA
SRX9149334 SRP259971 OTHER SINGLE
GSM4795048: K562 untreated rep2; Homo sapiens; OTHER
Sample: SRS7390124
BioProject: PRJNA630074
BioSample: SAMN16205937
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: K562 untreated
cell line: K562
rna probing reagent: None
Original files (1)
K562 untreated
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR12668785 248274587 17794781009 8090.8 K562_D2.fastq.gz, SRR12668785, SRR12668785.lite SRA
SRX9149335 SRP259971 OTHER SINGLE
GSM4795049: HepG2 untreated rep1; Homo sapiens; OTHER
Sample: SRS7390126
BioProject: PRJNA630074
BioSample: SAMN16205936
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: HepG2 untreated
cell line: HepG2
rna probing reagent: None
Original files (1)
HepG2 untreated
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR12668786 179816667 13601628483 5974.29 HepG2_D1.fastq.gz, SRR12668786, SRR12668786.lite SRA
SRX9149336 SRP259971 OTHER SINGLE
GSM4795050: HepG2 untreated rep2; Homo sapiens; OTHER
Sample: SRS7390127
BioProject: PRJNA630074
BioSample: SAMN16205935
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: HepG2 untreated
cell line: HepG2
rna probing reagent: None
Original files (1)
HepG2 untreated
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR12668787 206441539 15594924593 6898.27 HepG2_D2.fastq.gz, SRR12668787, SRR12668787.lite SRA
SRX9149337 SRP259971 OTHER SINGLE
GSM4795051: HeLa untreated rep1; Homo sapiens; OTHER
Sample: SRS7390128
BioProject: PRJNA630074
BioSample: SAMN16205939
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: HeLa untreated
cell line: HeLa
rna probing reagent: None
Original files (1)
HeLa untreated
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR12668788 208221981 15149746365 6805.22 HeLa_D1.fastq.gz, SRR12668788, SRR12668788.lite SRA
SRX9149338 SRP259971 OTHER SINGLE
GSM4795052: HeLa untreated rep2; Homo sapiens; OTHER
Sample: SRS7390129
BioProject: PRJNA630074
BioSample: SAMN16205934
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: HeLa untreated
cell line: HeLa
rna probing reagent: None
Original files (1)
HeLa untreated
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR12668789 152499397 11357747716 5212.05 HeLa_D2.fastq.gz, SRR12668789, SRR12668789.lite SRA

Linked Publications (2)

fSHAPE, fSHAPE-eCLIP, and SHAPE-eCLIP probe transcript regions that interact with specific proteins.
STAR protocols · 2021
Footprinting SHAPE-eCLIP Reveals Transcriptome-wide Hydrogen Bonds at RNA-Protein Interfaces.
Molecular cell · 2020

Data Files (41)

Accession File Name Stored Type Output Type Mapping Assembly Size Download
— HeLa_D1.fastq.gz OTHER 6.6 GB link
— HeLa_D2.fastq.gz OTHER 5.1 GB link
— HeLa_vitro_N1.fastq.gz OTHER 12.5 GB link
— HeLa_vitro_N2.fastq.gz OTHER 4.8 GB link
— HeLa_vivo_N1.fastq.gz OTHER 13.5 GB link
— HeLa_vivo_N2.fastq.gz OTHER 12.9 GB link
— HepG2_D1.fastq.gz OTHER 5.8 GB link
— HepG2_D2.fastq.gz OTHER 6.7 GB link
— HepG2_vitro_N1.fastq.gz OTHER 13.3 GB link
— HepG2_vitro_N2.fastq.gz OTHER 13.5 GB link
— HepG2_vivo_N1.fastq.gz OTHER 12.3 GB link
— HepG2_vivo_N2.fastq.gz OTHER 10.7 GB link
— K562_D1.fastq.gz OTHER 5.3 GB link
— K562_D2.fastq.gz OTHER 7.9 GB link
— K562_vitro_N1.fastq.gz OTHER 16.7 GB link
— K562_vitro_N2.fastq.gz OTHER 16.2 GB link
— K562_vivo_N1.fastq.gz OTHER 16.1 GB link
— K562_vivo_N2.fastq.gz OTHER 13.2 GB link
— MC_DMS1_Input_S48_L004_R1_001.fastq.gz OTHER 821.0 MB link
— MC_DMS1_IP_S49_L004_R1_001.fastq.gz OTHER 813.1 MB link
— MC_DMS2_Input_S50_L004_R1_001.fastq.gz OTHER 1017.6 MB link
— MC_DMS2_IP_S51_L004_R1_001.fastq.gz OTHER 932.9 MB link
— MC_NAI1_IP_S31_L007_R1_001.fastq.gz OTHER 1.2 GB link
— MC_NAI2_IP_S55_L008_R1_001.fastq.gz OTHER 1.2 GB link
— MC_noDMS1_Input_S52_L004_R1_001.fastq.gz OTHER 1.0 GB link
— MC_noDMS1_IP_S53_L004_R1_001.fastq.gz OTHER 1.0 GB link
— MC_noDMS2_Input_S54_L004_R1_001.fastq.gz OTHER 720.8 MB link
— MC_noDMS2_IP_S55_L004_R1_001.fastq.gz OTHER 811.1 MB link
— MC_noNAI1_Input_S3_L006_R1_001.fastq.gz OTHER 1.3 GB link
— MC_noNAI1_IP_S1_L006_R1_001.fastq.gz OTHER 1.5 GB link
— MC_noNAI2_Input_S4_L006_R1_001.fastq.gz OTHER 1.2 GB link
— MC_noNAI2_IP_S2_L006_R1_001.fastq.gz OTHER 937.5 MB link
— MC_vitro1_Input_S3_L002_R1_001.fastq.gz OTHER 1.7 GB link
— MC_vitro1_IP_S7_L002_R1_001.fastq.gz OTHER 897.5 MB link
— MC_vitro2_Input_S4_L002_R1_001.fastq.gz OTHER 1022.8 MB link
— MC_vitro2_IP_S8_L002_R1_001.fastq.gz OTHER 1.5 GB link
— MC_vivo1_Input_S1_L002_R1_001.fastq.gz OTHER 1.6 GB link
— MC_vivo1_IP_S5_L002_R1_001.fastq.gz OTHER 1.2 GB link
— MC_vivo2_Input_S2_L002_R1_001.fastq.gz OTHER 1.2 GB link
— MC_vivo2_IP_S6_L002_R1_001.fastq.gz OTHER 1.0 GB link
— SRR11682354.lite OTHER 16.7 GB link