GSE118347

Mutant FUS and ELAVL4 (HuD) aberrant crosstalk in Amyotrophic Lateral Sclerosis

1. Library strategy: PAR-CLIP
2. Sequencing data was converted using the bcl2fastq tool from the Illumina CASAVA package, followed by demultiplexing and 3’ adapter trimming using flexbar and Cutadapt .
3. To remove PCR duplicates, reads with identical sequence were collapsed, then we used FASTX Trimmer tool to remove random nucleotides from both ends of collapsed reads.
4. Reads shorter than 14 nucleotides were discarded.
5. BWA-based PARA-Suite aligner was used to align reads to GRCh38 genome and to a custom database of exon-exon junctions generated from Ensembl 89 transcriptome annotation.
6. We handled multi-mapping reads by keeping only those that mapped once with at least one T-C mismatch: mapping positions indicating T-C transitions were chosen as the correct ones.
7. Alignment files from each pair of replicates were combined and T-C transition were called using Bmix tool.
8. Only transitions supported by at least two reads from both replicates were kept.

Supplementary Files (2)

Dataset Citations (2)

Linked Publications (2)