biostudies-arrayexpressJernej UleHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-13328CLK 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' }biostudies-arrayexpressNucleic Acid Extraction - RNA extractions were performed from cell pellets using the Maxwell RSC simplyRNA kit (Promega) using a Maxwell RSC Instrument (Promega).Sample Collection - Samples were collected by trypsinising, spinning down, washing in PBS, spinning down and snap freezing on dry ice.Library Construction - RNA was fragmented using magnesium ions and heat, purified, and reverse transcribed using an oligo-dT primer with an Illumina P7 sequence and UMIs. A template switching oligo with the P5 sequence was included in the reaction. The library was then amplified with indexed Illumina i5/i7 primers.Sample Treatment - Samples were treated for 8 hours with either 1 uM CLK-IN-T3 or the equivalent volume of DMSO.Sequencing - Libraries were sequenced on a NovaSeq 6000 by the Advanced Sequencing Facility at The Francis Crick Institute.Growth Protocol - Cells were grown in DMEM+Glutamax+10% FBS and seeded such that they achieved 70% confluency on the morning of the experiment, with each sample being derived from 2 wells of a 6 well plate.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesSequence Alignment - All data was processed using the nf-core/rnaseq pipeline as described in the description of the accession.Data Transformation - All data was processed using the nf-core/rnaseq pipeline as described in the description of the accession. Quantification was performed using the STAR-Salmon section of the pipeline. No normalisation for the length of the transcript was applied.MetabolomicsUnknownTranscriptomicsGenomicsProteomicsMaxwell RSC InstrumentIllumina NovaSeq 6000RNA-seq of coding RNAHomo sapiensRupert FarawayJernej Ulefalse3' sequencing of nuclear and cytoplasmic fractions following treatment with a CLK inhibitorCLK 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' }2025-07-29T00:00:00Z2025-07-30T00:01:13.011Z2023-09-04T15:00:50.829ZE-MTAB-13328ERP150951EFO_0002944EFO_0004170EFO_0003789EFO_0004917EFO_0005518EFO_0003816EFO_0003738EFO_0004184EFO_0003969