GSE266924
GSE GEOExonuclease assisted mapping of protein-RNA interactions (ePRINT)
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Summary
RNA processing is a fundamental mode of gene regulation that is perturbed in a variety of diseases including cancer and neurodegenerative disorders. RNA-binding proteins (RBPs) regulate key aspects of RNA processing including alternative splicing, mRNA degradation and localization by physically binding RNA molecules. Current methods to map these interactions, such as CLIP, rely on purifying single proteins at a time. We have developed a new method (ePRINT) to map RBP-RNA interaction networks on a global scale without purifying individual RBPs. By deploying the exoribonuclease XRN1, ePRINT allows precise mapping of the 5â end of the RBP binding site and uncovers direct and indirect targets of an RBP of interest. Importantly, ePRINT can also uncover RBPs that are differentially activated between cell fate transitions, including neural progenitor differentiation into neurons. Given its versatility, ePRINT has vast application potential as an investigative tool for RNA regulation in development, health and disease.
Overall Design
The following are sequencing data for an enhanced crosslinking immunoprecipitation-seq experiments. The sets contain the RNAs directly crosslinked to FUS with a size-matched control used as an input.
Analysis (5 steps)
View Data Processing- Read1 data was processed using Skipper, available at: https://github.com/yeolab/skipper
- Reads were trimmed for adapter sequences and barcode sequences (eCLIP samples) using skewer.
- Unique Molecular Identifiers (UMIs) were extracted from raw sequencing reads with fastp
- Extracted reads were aligned using STAR: --alignEndsType EndToEnd --genomeDir {params.star_sjdb} --genomeLoad NoSharedMemory --outBAMcompression 10 --outFileNamePrefix {params.outprefix} --winAnchorMultimapNmax 100 --outFilterMultimapNmax 100 --outFilterMultimapScoreRange 1 --outSAMmultNmax 1 --outMultimapperOrder Random --outFilterScoreMin 10 --outFilterType BySJout --limitOutSJcollapsed 5000000 --outReadsUnmapped None --outSAMattrRGline ID:{wildcards.replicate_label} --outSAMattributes All --outSAMmode Full --outSAMtype BAM Unsorted --outSAMunmapped Within --readFilesCommand zcat --outStd Log --readFilesIn {input.fq} --runMode alignReads --runThreadN {threads}
- Custom scripts called reproducible enriched windows and repetitive elements as part of Skipper
Supplementary Files (3)
GEO Samples (4)
SRA Experiments (4) and Runs (4)
Total: 6759 MBSample attributes
Original files (1)
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR28928317 | 20399053 | 4120608706 | 1467.72 | FUS_IN1_S1_L001_R1_001.fastq.gz, FUS_IN1_S1_L001_R2_001.fastq.gz, SRR… | SRA |
Sample attributes
Original files (1)
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR28928316 | 20624792 | 4166207984 | 1504.66 | FUS_IN2_S2_L001_R1_001.fastq.gz, FUS_IN2_S2_L001_R2_001.fastq.gz, SRR… | SRA |
Sample attributes
Original files (1)
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR28928315 | 26966003 | 5447132606 | 1946.71 | FUS_IP1_S3_L001_R1_001.fastq.gz, FUS_IP1_S3_L001_R2_001.fastq.gz, SRR… | SRA |
Sample attributes
Original files (1)
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR28928314 | 25214786 | 5093386772 | 1839.54 | FUS_IP2_S4_L001_R1_001.fastq.gz, FUS_IP2_S4_L001_R2_001.fastq.gz, SRR… | SRA |