3' sequencing of nuclear and cytoplasmic fractions following treatment with a CLK inhibitor

CLK kinases phosphorylate the SR domains of SR proteins. The phosphorylation state controls the localisation of SR proteins, with hypo-phosphorylated SR proteins being more enriched in nuclear speckles. We identified a set of mRNAs that are bound by SR proteins in the nucleus, and we wondered whether the activity of CLK kinases would alter the nuclear export of those mRNAs. We therefore treated HeLa cells with the CLK inhibitor CLK-IN-T3 or with DMSO for 8 hours and then collected nuclear and cytoplasmic fractions. We sequenced the 3' ends of poly-adenylated mRNAs in these fractions. The samples in this accession have been trimmed to remove Illumina adapters, 3' poly-A stretches, 5' G stretches from the TSO oligo and the UMIs have been moved to the header. The data was then processed using the following nf-core/rnaseq call: nextflow run nf-core/rnaseq \ --input 'samplesheet.csv' \ --fasta '/camp/lab/ulej/home/users/farawar/genomes/hs/fasta/GRCh38.primary_assembly.genome.fa' \ --gtf '/camp/lab/ulej/home/users/farawar/genomes/hs/annotation/gencode.v29.annotation.gtf' \ --salmon_index '/camp/lab/ulej/home/users/farawar/genomes/hs/salmon_index/salmon_index' \ --gencode \ --pseudo_aligner salmon \ -resume \ -profile crick \ --outdir nf-core \ -c extraconfig.config With the extra config file containing the following: withName: '.*:QUANTIFY_STAR_SALMON:SALMON_QUANT' { ext.args = '--noLengthCorrection' }