Multiplexed transcriptome discovery of RNA-binding protein binding sites by antibody-barcode eCLIP.
Daniel A Lorenz, Hsuan-Lin Her, Kylie A Shen, Katie Rothamel, Kasey R Hutt, Allan C Nojadera, Stephanie C Bruns, Sergei A Manakov, Brian A Yee, Karen B Chapman, Gene W Yeo
Nature methods · 2023 · Vol. 20 (1) · pp. 65-69
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.
Linked datasets 1
Multiplexed transcriptome discovery of RNA binding protein binding sites by antibody-barcode eCLIP
Homo sapiens
18 data files
| File | Type | Size |
|---|---|---|
| HEK293_RBFOX2_rep1.fastq.gz | OTHER | 806.2 MB |
| HEK293_RBFOX2_rep2.fastq.gz | OTHER | 487.3 MB |
| HEK293_rep1.fastq.gz | OTHER | 7.2 GB |
| HEK293_rep2.fastq.gz | OTHER | 5.1 GB |
| K562_rep1.fastq.gz | OTHER | 4.8 GB |
| K562_rep4.fastq.gz | OTHER | 5.0 GB |
| K562_rep6.fastq.gz | OTHER | 3.8 GB |
| K562_SLBP_rep1.fastq.gz | OTHER | 911.3 MB |
| K562_SLBP_rep2.fastq.gz | OTHER | 382.0 MB |
| SRR19547039_GSM6214400 | OTHER | 7.2 GB |
| SRR19547040_GSM6214399 | OTHER | 3.8 GB |
| SRR19547041_GSM6214398 | OTHER | 5.0 GB |
| SRR19547042_GSM6214401 | OTHER | 5.1 GB |
| SRR19547043_GSM6214397 | OTHER | 381.0 MB |
| SRR19547044_GSM6214396 | OTHER | 911.0 MB |
| SRR19547045_GSM6214395 | OTHER | 487.0 MB |
| SRR19547046_GSM6214394 | OTHER | 806.0 MB |
| SRR21487073_GSM6561051 | OTHER | 4.8 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.
| Accession | Source | Title |
|---|---|---|
| GSE122425 | GSE · GEO GEO ↗ | Effects of NSUN2 deficiency on the mRNA 5-methylcytosine modification and gene expression profile in HEK293 cells (RNA-Seq) |
| ENCSR000AEL | ENCSR · ENCODE | No title in the index |
| GSE205536 | GSE · GEO GEO ↗ | Multiplexed transcriptome discovery of RNA binding protein binding sites by antibody-barcode eCLIP |
Analysis pipelines 2
| Pipeline | Assay | Steps | Dataset |
|---|---|---|---|
| GSE122425 RNA-seq Data Processing geo_data_processing | RNA-seq | 5 | GSE122425 |
| GSE205536 eCLIP Data Processing geo_data_processing | eCLIP | 13 | GSE205536 |
Funding 1 grant
| Grant | Funder |
|---|---|
| T32 CA067754 | NCI NIH HHS (United States) |