Multiplexed transcriptome discovery of RNA-binding protein binding sites by antibody-barcode eCLIP.
Abstract
Ultraviolet crosslinking and immunoprecipitation (CLIP) methodologies enable the identification of RNA binding sites of RNA-binding proteins (RBPs). Despite improvements in the library preparation of RNA fragments, the enhanced CLIP (eCLIP) protocol requires 4 days of hands-on time and lacks the ability to process several RBPs in parallel. We present a new method termed antibody-barcode eCLIP that utilizes DNA-barcoded antibodies and proximity ligation of the DNA oligonucleotides to RBP-protected RNA fragments to interrogate several RBPs simultaneously. We observe performance comparable with that of eCLIP with the advantage of dramatically increased scaling while maintaining the same material requirement of a single eCLIP experiment.
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Linked Datasets (1)
Multiplexed transcriptome discovery of RNA binding protein binding sites by antibody-barcode eCLIP
Homo sapiens27 data files
| File | Type | Size |
|---|---|---|
| HEK293_RBFOX2_rep1.fastq.gz | OTHER | 806.2 MB |
| HEK293_RBFOX2_rep1.fastq.gz | OTHER | 806.2 MB |
| HEK293_RBFOX2_rep1.fastq.gz | OTHER | 806.2 MB |
| HEK293_RBFOX2_rep2.fastq.gz | OTHER | 487.3 MB |
| HEK293_RBFOX2_rep2.fastq.gz | OTHER | 487.3 MB |
| HEK293_RBFOX2_rep2.fastq.gz | OTHER | 487.3 MB |
| HEK293_rep1.fastq.gz | OTHER | 7.2 GB |
| HEK293_rep1.fastq.gz | OTHER | 7.2 GB |
| HEK293_rep1.fastq.gz | OTHER | 7.2 GB |
| HEK293_rep2.fastq.gz | OTHER | 5.1 GB |
| HEK293_rep2.fastq.gz | OTHER | 5.1 GB |
| HEK293_rep2.fastq.gz | OTHER | 5.1 GB |
| K562_rep1.fastq.gz | OTHER | 4.8 GB |
| K562_rep1.fastq.gz | OTHER | 4.8 GB |
| K562_rep1.fastq.gz | OTHER | 4.8 GB |
| K562_rep4.fastq.gz | OTHER | 5.0 GB |
| K562_rep4.fastq.gz | OTHER | 5.0 GB |
| K562_rep4.fastq.gz | OTHER | 5.0 GB |
| K562_rep6.fastq.gz | OTHER | 3.8 GB |
| K562_rep6.fastq.gz | OTHER | 3.8 GB |
| K562_rep6.fastq.gz | OTHER | 3.8 GB |
| K562_SLBP_rep1.fastq.gz | OTHER | 911.3 MB |
| K562_SLBP_rep1.fastq.gz | OTHER | 911.3 MB |
| K562_SLBP_rep1.fastq.gz | OTHER | 911.3 MB |
| K562_SLBP_rep2.fastq.gz | OTHER | 382.0 MB |
| K562_SLBP_rep2.fastq.gz | OTHER | 382.0 MB |
| K562_SLBP_rep2.fastq.gz | OTHER | 382.0 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.
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