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
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.
Linked datasets 7
Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes [STAMP_new_eclip]
Homo sapiens
10 data files
| File | Type | Size |
|---|---|---|
| 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_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 |
| 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 |
Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes
Homo sapiens
Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes [tia1_eclip]
Homo sapiens
10 data files
| File | Type | Size |
|---|---|---|
| TIA_293T.rep1_clip.r1.reformatted.fq.gz | RIP-Seq | 291.5 MB |
| TIA_293T.rep1_clip.r1.reformatted.fq.gz | RIP-Seq | 291.5 MB |
| 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.rep1_input.NIL.r1.fq.gz | RIP-Seq | 460.5 MB |
| TIA_293T.rep1_input.NIL.r1.fq.gz | RIP-Seq | 460.5 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 |
| TIA_293T.rep2_clip.r1.reformatted.fq.gz | RIP-Seq | 178.8 MB |
| TIA_293T.rep2_clip.r1.reformatted.fq.gz | RIP-Seq | 178.8 MB |
Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes [RNA-seq]
Homo sapiens
10 data files
| File | Type | Size |
|---|---|---|
| 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_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 |
| 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 |
Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes [scRNA-seq]
Homo sapiens
10 data files
| File | Type | Size |
|---|---|---|
| control_STAMP_possorted_genome_bam.bam | RNA-Seq | 12.0 GB |
| 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_control_STAMP_possorted_genome_bam.bam | RNA-Seq | 8.6 GB |
| NPC_HEK_RBFOX2_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 |
| RBP_STAMP_possorted_genome_bam.bam | RNA-Seq | 18.6 GB |
| RPS2_STAMP_possorted_genome_bam.bam | RNA-Seq | 12.3 GB |
| RPS2_STAMP_possorted_genome_bam.bam | RNA-Seq | 12.3 GB |
Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes [NP]
Homo sapiens
10 data files
| File | Type | Size |
|---|---|---|
| APOBEC_cDNA_all_pass.fastq.gz | RNA-Seq | 7.7 GB |
| APOBEC_cDNA_all_pass.fastq.gz | RNA-Seq | 7.7 GB |
| APOBEC_dRNA.fastq.gz | RNA-Seq | 545.2 MB |
| APOBEC_dRNA.fastq.gz | RNA-Seq | 545.2 MB |
| RBFOX2_cDNA_all_pass.fastq.gz | RNA-Seq | 21.1 GB |
| RBFOX2_cDNA_all_pass.fastq.gz | RNA-Seq | 21.1 GB |
| RBFOX2_dRNA.fastq.gz | RNA-Seq | 1.2 GB |
| RBFOX2_dRNA.fastq.gz | RNA-Seq | 1.2 GB |
| RBFOX2_dRNA.fastq.gz | RNA-Seq | 1.2 GB |
| SRR12389276.lite | RNA-Seq | 21.1 GB |
Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes [STAMP_pacbio]
Homo sapiens
10 data files
| File | Type | Size |
|---|---|---|
| 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_5779_APO1_1_demultiplex.bc1001_BAK8A_OA__bc1001_B… | OTHER | 327.6 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_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 |
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.
| Accession | Source | Title |
|---|---|---|
| GSE109423 | GSE · GEO GEO ↗ | A transcriptome-wide divergence in protein translation scales with LIN28B expression |
| GSE94460 | GSE · GEO GEO ↗ | Ribosome profiling of HEK293 cells. |
| GSE112353 | GSE · GEO GEO ↗ | Active ribosome profiling with RiboLace and standard ribosome profiling in HEK-293 cells |
Funding 8 grants
| Grant | Funder |
|---|---|
| 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) |