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Robust single-cell discovery of RNA targets of RNA-binding proteins and ribosomes.

Kristopher W Brannan, Isaac A Chaim, Ryan J Marina, Brian A Yee, Eric R Kofman, Daniel A Lorenz, Pratibha Jagannatha, Kevin D Dong, Assael A Madrigal, Jason G Underwood, Gene W Yeo
Nature methods · 2021 · Vol. 18 (5) · pp. 507-519
PubMed DOI PMC Full Text

Abstract

RNA-binding proteins (RBPs) are critical regulators of gene expression and RNA processing that are required for gene function. Yet the dynamics of RBP regulation in single cells is unknown. To address this gap in understanding, we developed STAMP (Surveying Targets by APOBEC-Mediated Profiling), which efficiently detects RBP-RNA interactions. STAMP does not rely on ultraviolet cross-linking or immunoprecipitation and, when coupled with single-cell capture, can identify RBP-specific and cell-type-specific RNA-protein interactions for multiple RBPs and cell types in single, pooled experiments. Pairing STAMP with long-read sequencing yields RBP target sites in an isoform-specific manner. Finally, Ribo-STAMP leverages small ribosomal subunits to measure transcriptome-wide ribosome association in single cells. STAMP enables the study of RBP-RNA interactomes and translational landscapes with unprecedented cellular resolution.

Publication Types

["Journal Article", "Research Support, N.I.H., Extramural"]

Keywords

[]

MeSH Terms

["Animals", "Binding Sites", "Gene Expression Profiling", "HEK293 Cells", "Humans", "Nanopore Sequencing", "RNA", "RNA-Binding Proteins", "Sequence Analysis, RNA", "Single-Cell Analysis", "Transcriptome"]

Funding

U24 HG009889 NHGRI NIH HHS (United States)
R01 HG004659 NHGRI NIH HHS (United States)
U41 HG009889 NHGRI NIH HHS (United States)
K22 NS112678 NINDS NIH HHS (United States)
T32 GM008666 NIGMS NIH HHS (United States)
T32 GM008806 NIGMS NIH HHS (United States)
K12 GM068524 NIGMS NIH HHS (United States)
F31 NS111859 NINDS NIH HHS (United States)

Linked Datasets (7)

GSE155726 GSE via ncbi_elink
GEO

Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes [scRNA-seq]

Homo sapiens
5 data files
FileTypeSize
control_STAMP_possorted_genome_bam.bam RNA-Seq 12.0 GB
NPC_HEK_control_STAMP_possorted_genome_bam.bam RNA-Seq 8.6 GB
NPC_HEK_RBFOX2_STAMP_possorted_genome_bam.bam RNA-Seq 8.6 GB
RBP_STAMP_possorted_genome_bam.bam RNA-Seq 18.6 GB
RPS2_STAMP_possorted_genome_bam.bam RNA-Seq 12.3 GB
GSE155728 GSE via ncbi_elink
GEO

Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes [tia1_eclip]

Homo sapiens
3 data files
FileTypeSize
TIA_293T.rep1_clip.r1.reformatted.fq.gz RIP-Seq 291.5 MB
TIA_293T.rep1_input.NIL.r1.fq.gz RIP-Seq 460.5 MB
TIA_293T.rep2_clip.r1.reformatted.fq.gz RIP-Seq 178.8 MB
GSE166402 GSE via ncbi_elink
GEO

Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes [STAMP_new_eclip]

Homo sapiens
9 data files
FileTypeSize
NRBF_1_S3_L001_R1_001.fastq.gz RIP-Seq 567.9 MB
NRBF_2_S4_L001_R1_001.fastq.gz RIP-Seq 583.6 MB
NTIA_1_S1_L001_R1_001.fastq.gz RIP-Seq 636.0 MB
NTIA_2_S2_L001_R1_001.fastq.gz RIP-Seq 333.4 MB
PRBF_1_S9_L001_R1_001.fastq.gz RIP-Seq 1.0 GB
PRBF_2_S10_L001_R1_001.fastq.gz RIP-Seq 888.1 MB
PTIA_1_S7_L001_R1_001.fastq.gz RIP-Seq 597.6 MB
PTIA_2_S8_L001_R1_001.fastq.gz RIP-Seq 878.5 MB
SRR13663712.lite RIP-Seq 333.4 MB
GSE155649 GSE via ncbi_elink
GEO

Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes [RNA-seq]

Homo sapiens
77 data files
FileTypeSize
Apobec_plusT_1_S30_L003_R1_001.fastq.gz OTHER 564.3 MB
Apobec_plusT_2_S31_L003_R1_001.fastq.gz OTHER 631.7 MB
Apobec-T_1_S28_L003_R1_001.fastq.gz OTHER 614.7 MB
Apobec-T_2_S29_L003_R1_001.fastq.gz OTHER 814.8 MB
ApoControl-0_S7_L001_R1_001.fastq.gz OTHER 1.5 GB
ApoControl-1000_S21_L002_R1_001.fastq.gz OTHER 1.5 GB
ApoControl-50_S14_L002_R1_001.fastq.gz OTHER 1.3 GB
RBFOX2-0_S6_L001_R1_001.fastq.gz OTHER 1.4 GB
RBFOX2-1000_S20_L002_R1_001.fastq.gz OTHER 1.6 GB
RBFOX2-50_S13_L002_R1_001.fastq.gz OTHER 1.4 GB
RPS2-0_S4_L001_R1_001.fastq.gz OTHER 1.1 GB
RPS2-1000_S18_L002_R1_001.fastq.gz OTHER 1.4 GB
RPS2-50_S11_L001_R1_001.fastq.gz OTHER 1.5 GB
RPS3-0_S5_L001_R1_001.fastq.gz OTHER 1.8 GB
RPS3-1000_S19_L002_R1_001.fastq.gz OTHER 1.8 GB
Sample_10_S60_L006_R1_001.fastq.gz OTHER 925.3 MB
Sample11_S29_merged.fastq.gz OTHER 133.9 MB
Sample12_S30_merged.fastq.gz OTHER 131.5 MB
Sample13_S31_merged.fastq.gz OTHER 148.9 MB
Sample14_S13_merged.fastq.gz OTHER 457.9 MB
Sample15_S14_merged.fastq.gz OTHER 349.1 MB
Sample16_S32_merged.fastq.gz OTHER 92.0 MB
Sample17_S15_merged.fastq.gz OTHER 357.1 MB
Sample18_S16_merged.fastq.gz OTHER 271.3 MB
Sample19_S17_merged.fastq.gz OTHER 422.5 MB
Sample1_S23_merged.fastq.gz OTHER 225.8 MB
Sample20_S18_merged.fastq.gz OTHER 302.1 MB
Sample21_S33_merged.fastq.gz OTHER 154.6 MB
Sample22_S34_merged.fastq.gz OTHER 125.2 MB
Sample23_S35_merged.fastq.gz OTHER 260.5 MB
Sample24_S36_merged.fastq.gz OTHER 132.1 MB
Sample25_S19_merged.fastq.gz OTHER 273.1 MB
Sample26_S20_merged.fastq.gz OTHER 241.7 MB
Sample27_S37_merged.fastq.gz OTHER 146.2 MB
Sample28_S21_merged.fastq.gz OTHER 344.7 MB
Sample29_S38_merged.fastq.gz OTHER 265.3 MB
Sample2_S24_merged.fastq.gz OTHER 172.2 MB
Sample30_S39_merged.fastq.gz OTHER 138.2 MB
Sample31_S40_merged.fastq.gz OTHER 139.6 MB
Sample32_S22_merged.fastq.gz OTHER 237.7 MB
Sample_33_S61_L006_R1_001.fastq.gz OTHER 440.1 MB
Sample_34_S62_L006_R1_001.fastq.gz OTHER 556.8 MB
Sample_35_S63_L006_R1_001.fastq.gz OTHER 882.0 MB
Sample_36_S64_L006_R1_001.fastq.gz OTHER 538.0 MB
Sample_37_S65_L006_R1_001.fastq.gz OTHER 664.4 MB
Sample_38_S66_L006_R1_001.fastq.gz OTHER 963.6 MB
Sample_39_S67_L006_R1_001.fastq.gz OTHER 715.0 MB
Sample_3_S57_L006_R1_001.fastq.gz OTHER 980.1 MB
Sample_40_S68_L006_R1_001.fastq.gz OTHER 730.7 MB
Sample41_S41_merged.fastq.gz OTHER 63.0 MB
Sample42_S42_merged.fastq.gz OTHER 124.1 MB
Sample4_S25_merged.fastq.gz OTHER 211.6 MB
Sample5_S26_merged.fastq.gz OTHER 205.2 MB
Sample_6_S58_L006_R1_001.fastq.gz OTHER 587.0 MB
Sample7_S27_merged.fastq.gz OTHER 209.6 MB
Sample8_S28_merged.fastq.gz OTHER 226.2 MB
Sample_9_S59_L006_R1_001.fastq.gz OTHER 720.2 MB
SLBP_0_48hr_A_merged_R1.fastq.gz OTHER 1.2 GB
SLBP_0_48hr_B_merged_R1.fastq.gz OTHER 1.5 GB
SLBP_0_48hr_C_merged_R1.fastq.gz OTHER 1.7 GB
SLBP_0_72hr_A_merged_R1.fastq.gz OTHER 1.2 GB
SLBP_0_72hr_B_merged_R1.fastq.gz OTHER 1.2 GB
SLBP_0_72hr_C_merged_R1.fastq.gz OTHER 1.1 GB
SLBP_1000_72hr_A_merged_R1.fastq.gz OTHER 937.1 MB
SLBP_1000_72hr_B_merged_R1.fastq.gz OTHER 1.2 GB
SLBP_1000_72hr_C_merged_R1.fastq.gz OTHER 1.1 GB
TI_55_S13_L001_R1_001.fastq.gz OTHER 883.8 MB
TI_56_S14_L001_R1_001.fastq.gz OTHER 241.8 MB
TI_58_S15_L001_R1_001.fastq.gz OTHER 262.8 MB
TI_59_S16_L001_R1_001.fastq.gz OTHER 718.1 MB
TI_8_S6_L001_R1_001.fastq.gz RNA-Seq 958.8 MB
Tia1_0ng_1_S40_L003_R1_001.fastq.gz OTHER 951.1 MB
Tia1_0ng_2_S41_L003_R1_001.fastq.gz OTHER 708.4 MB
Tia1_1000ng_1_S14_L001_R1_001.fastq.gz OTHER 486.1 MB
Tia1_1000ng_2_S27_L002_R1_001.fastq.gz OTHER 581.7 MB
Tia1_50ng_1_S42_L003_R1_001.fastq.gz OTHER 722.9 MB
Tia1_50ng_2_S13_L001_R1_001.fastq.gz OTHER 792.6 MB
GSE155729 GSE via ncbi_elink
GEO

Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes

Homo sapiens
GSE166404 GSE via ncbi_elink
GEO

Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes [STAMP_pacbio]

Homo sapiens
30 data files
FileTypeSize
CCS_Demux_5759_APO1_1_demultiplex.bc1001_BAK8A_OA__bc1001_B… OTHER 32.0 MB
CCS_Demux_5759_APO1_2_demultiplex.bc1015_BAK8B_OA__bc1015_B… OTHER 29.7 MB
CCS_Demux_5759_APO1_3_demultiplex.bc1016_BAK8B_OA__bc1016_B… OTHER 20.7 MB
CCS_Demux_5759_RBFOX_1_demultiplex.bc1020_BAK8B_OA__bc1020_… OTHER 12.6 MB
CCS_Demux_5759_RBFOX_2_demultiplex.bc1021_BAK8B_OA__bc1021_… OTHER 19.5 MB
CCS_Demux_5759_RBFOX_3_demultiplex.bc1022_BAK8B_OA__bc1022_… OTHER 28.2 MB
CCS_Demux_5779_APO1_1_demultiplex.bc1001_BAK8A_OA__bc1001_B… OTHER 327.6 MB
CCS_Demux_5779_APO1_2_demultiplex.bc1015_BAK8B_OA__bc1015_B… OTHER 291.7 MB
CCS_Demux_5779_APO1_3_demultiplex.bc1016_BAK8B_OA__bc1016_B… OTHER 228.5 MB
CCS_Demux_5779_RBFOX_1_demultiplex.bc1020_BAK8B_OA__bc1020_… OTHER 141.2 MB
CCS_Demux_5779_RBFOX_2_demultiplex.bc1021_BAK8B_OA__bc1021_… OTHER 208.6 MB
CCS_Demux_5779_RBFOX_3_demultiplex.bc1022_BAK8B_OA__bc1022_… OTHER 293.3 MB
CCS_Demux_5896_APO1_1_demultiplex.bc1001_BAK8A_OA__bc1001_B… OTHER 52.7 MB
CCS_Demux_5896_APO1_2_demultiplex.bc1015_BAK8B_OA__bc1015_B… OTHER 63.0 MB
CCS_Demux_5896_APO1_3_demultiplex.bc1016_BAK8B_OA__bc1016_B… OTHER 46.5 MB
CCS_Demux_5896_RBFOX_1_demultiplex.bc1020_BAK8B_OA__bc1020_… OTHER 39.6 MB
CCS_Demux_5896_RBFOX_2_demultiplex.bc1021_BAK8B_OA__bc1021_… OTHER 55.5 MB
CCS_Demux_5896_RBFOX_3_demultiplex.bc1022_BAK8B_OA__bc1022_… OTHER 60.4 MB
CCS_Demux_6465_APO1_1_demultiplex.bc1001_BAK8A_OA__bc1001_B… OTHER 37.6 MB
CCS_Demux_6465_APO1_2_demultiplex.bc1015_BAK8B_OA__bc1015_B… OTHER 55.7 MB
CCS_Demux_6465_APO1_3_demultiplex.bc1016_BAK8B_OA__bc1016_B… OTHER 37.0 MB
CCS_Demux_6465_RBFOX_1_demultiplex.bc1020_BAK8B_OA__bc1020_… OTHER 38.8 MB
CCS_Demux_6465_RBFOX_2_demultiplex.bc1021_BAK8B_OA__bc1021_… OTHER 49.2 MB
CCS_Demux_6465_RBFOX_3_demultiplex.bc1022_BAK8B_OA__bc1022_… OTHER 52.9 MB
CCS_Demux_6499_APO1_1_demultiplex.bc1001_BAK8A_OA__bc1001_B… OTHER 43.8 MB
CCS_Demux_6499_APO1_2_demultiplex.bc1015_BAK8B_OA__bc1015_B… OTHER 34.3 MB
CCS_Demux_6499_APO1_3_demultiplex.bc1016_BAK8B_OA__bc1016_B… OTHER 28.8 MB
CCS_Demux_6499_RBFOX_1_demultiplex.bc1020_BAK8B_OA__bc1020_… OTHER 17.3 MB
CCS_Demux_6499_RBFOX_2_demultiplex.bc1021_BAK8B_OA__bc1021_… OTHER 27.2 MB
CCS_Demux_6499_RBFOX_3_demultiplex.bc1022_BAK8B_OA__bc1022_… OTHER 39.1 MB
GSE155708 GSE via ncbi_elink
GEO

Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes [NP]

Homo sapiens
6 data files
FileTypeSize
APOBEC_cDNA_all_pass.fastq.gz RNA-Seq 7.7 GB
APOBEC_dRNA.fastq.gz RNA-Seq 545.2 MB
RBFOX2_cDNA_all_pass.fastq.gz RNA-Seq 21.1 GB
RBFOX2_dRNA.fastq.gz RNA-Seq 1.2 GB
SRR12389274 RNA-Seq 7.7 GB
SRR12389276.lite RNA-Seq 21.1 GB

Potentially Related Datasets (3)

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.

GSE94460 GSE GEO
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Analysis Pipelines (9)

GSE112353 Ribo-seq Data Processing 5 steps
Ribo-seq geo_data_processing GSE112353
GSE155649 RNA-seq Data Processing 6 steps
RNA-seq geo_data_processing GSE155649
GSE155708 Data Processing 11 steps
geo_data_processing GSE155708
GSE155726 scRNA-seq Data Processing 12 steps
scRNA-seq geo_data_processing GSE155726
GSE155728 eCLIP Data Processing 21 steps
eCLIP geo_data_processing GSE155728
GSE155729 Data Processing 6 steps
geo_data_processing GSE155729
GSE166402 eCLIP Data Processing 18 steps
eCLIP geo_data_processing GSE166402
GSE166404 PacBio sequencing Data Processing 9 steps
PacBio sequencing geo_data_processing GSE166404
GSE94460 Ribo-seq Data Processing 4 steps
Ribo-seq geo_data_processing GSE94460