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167 results for “mRNA decay”
Additional Data: Poised PABP-RNA hubs implement signal-dependent mRNA decay in development
<p>This repository contains processed data resulting from iCLIP experiments that were analysed in the following paper:"<strong>Poised PABP-RNA hubs implement signal-dependent mRNA decay in development</strong>"<br>The paper is published at Nature Structural and Molecular BIology.</p> <h2><br>Archived data</h2> <p>Data archived in this repository include:</p> <ol> <li>Data derived from iCLIP experiments targeting LIN28A, PABPC1, and PABPC4, that were analysed in the manuscript (see iCLIP.zip). Raw data is available from ENA, with the accession code PRJEB60519. <ol> <li>Sample descriptions are given in iCLIP-SampleAnnotation.csv</li> <li>Crosslink files in BED6 format (individual replicates and merged replicates)</li> <li>Peak files generated with the Clippy peak caller in BED6 format</li> <li>K-mer enrichment around high-confidence crosslink sites in the 3'-UTRs, calculated by the PEKA software</li> </ol> </li> <li>Expression values (salmon quantfiles) for 3'-seq experiments, specified in "QuantseqExperimentsAnnotation.tsv", are available in "SalmonQuantfiles.zip". Raw data is available from ENA, with the accession code PRJEB60519.</li> <li>Source code of the nextflow pipeline, which was used on the iMaps webserver to analyse iCLIP data and produce the files archived here (see imaps-nf-0.30.zip).</li> <li>A list of naive genes, that were analysed in the manuscript (see NaiveGeneIds.csv).</li> </ol> <h2>Details on iCLIP data generation</h2> <p>iCLIP data for LIN28A-WT (in 2iL and FGF2 treated cells), LIN28A-S200A (in FGF2 treated cells) as well as for PABPC1 and PABPC4 (in LIN28A KO cells with and without LIN28A overexpression), were analysed on iMaps Goodwright server (<a href="https://imaps.goodwright.com/">https://imaps.goodwright.com/</a>). The LIN28A iCLIPs were analysed on 18th of July, 2022; the PABPC iCLIPs were analysed on 26th of December, 2022. The code and settings used in the pipeline (release v0.30) can be viewed at <a href="https://github.com/goodwright/imaps-nf">https://github.com/goodwright/imaps-nf </a>, and is also archived here - (imaps-nf-0.30.zip)<br> </p> <ul> <li>First, reads were demultiplexed using Ultraplex and barcodes were trimmed from the reads. The default Ultraplex settings were applied, as denoted below:</li> </ul> <blockquote> <p>adapter='AGATCGGAAGAGCGGTTCAG'<br>adapter2='AGATCGGAAGAGCGTCGTG'<br>barcodes='barcode.csv',<br>final_min_length=20<br>fiveprimemismatches=1<br>ignore_no_match=False<br>ignore_space_warning=False<br>inputfastq='MOD4878A1-merged.fastq.gz',<br>keep_barcode=False,<br>min_trim=3,<br>outputprefix='demux',<br>phredquality=30,<br>phredquality_5_prime=0,<br>sbatchcompression=False,<br>threads=10,<br>threeprimemismatches=0,<br>ultra=False</p> </blockquote> <p> </p> <ul> <li>TrimGalore was used to run FASTQC and quality trim the reads and remove reads with length less than 10 nt:</li> </ul> <blockquote> <p>trim_galore --fastqc --length 10 -q 20 --cores 8 --gzip file.fastq.gz</p> </blockquote> <p> </p> <ul> <li>Reads were then premapped to rRNA, tRNA sequences referred to as small RNA, smRNA, using mouse genome build (GRCm39 GENCODE M28 annotation) with Bowtie v1.3.0 (Langmead et al., 2009)</li> </ul> <blockquote> <p>bowtie --threads 12 --sam -x $INDEX -q --un file.unmapped.fastq -v 2 -m 100 --norc --best --strata file.fq.gz 2</p> </blockquote> <p> </p> <ul> <li>Reads that did not map with Bowtie were then aligned with STAR v2.7.9a (Dobin et al., 2013) to mouse genome build (GRCm39 GENCODE M28 annotation).</li> </ul> <blockquote> <p>STAR \<br>--genomeDir star \<br>--readFilesIn file.unmapped.fastq.gz \<br>--runThreadN 12 \<br>--outFileNamePrefix 1_R1. \<br>\<br>--sjdbGTFfile Homo_sapiens_filtered.gtf \<br>--outSAMattrRGline 'ID:1_R1' 'SM:1_R1' \<br> --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM --outFilterMultimapNmax 1 --outFilterMultimapScoreRange 1 --outSAMattributes All --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterType BySJout --alignIntronMin 20 --alignIntronMax 1000000 --outFilterScoreMin 10 --alignEndsType Extend5pOfRead1 --twopassMode Basic</p> </blockquote> <p> </p> <ul> <li>PCR-duplicates were removed using UMI-tools (Smith, Heger and Sudbery, 2017)</li> </ul> <blockquote> <p>java -jar /UMICollapse/umicollapse.jar \<br> bam \<br> -i file.Aligned.sortedByCoord.out.bam \<br> -o file.dedup.bam \<br> --umi-sep rbc:</p> </blockquote> <p> </p> <ul> <li>The nucleotide preceding each sequencing read was assigned as the crosslink event.</li> </ul> <p> </p> <ul> <li>Peaks of crosslinking signal were identified with Clippy v1.4.1, using the default settings.</li> </ul> <p> </p> <ul> <li>Obtained peaks and crosslink sites were used to run PEKA v1.0.0 (Kuret et al., 2022), using the default settings.</li> </ul> <p> </p> <ul> <li>For Clippy and PEKA, the GENCODE primary assembly annotation M28 was filtered to retain only entries with transcript support level 1 or 2, in genes where such transcripts were available, and used to produce a segmentation file with the <em>get_segments</em> function from the iCount tool (Curk, 2019).</li> </ul> <p> </p> <ul> <li>All files generated during data processing are available from the iMaps Goodwright webserver for analysis of CLIP data (see <a href="https://imaps.goodwright.com/collections/882635250203/">https://imaps.goodwright.com/collections/882635250203/</a> and <a href="https://imaps.goodwright.com/collections/340215254997/">https://imaps.goodwright.com/collections/340215254997/</a> for LIN28A and PABPC1/4 iCLIPs, respectively).</li> </ul> <h2>Source data</h2> <p>Raw sequencing reads, from which the data enclosed here were derived, are accessible at ENA (PRJEB60519).<br>The raw sequencing reads and all data produced by the analysis pipeline is also available at the iMaps webserver (see <a href="https://imaps.goodwright.com/collections/882635250203/">https://imaps.goodwright.com/collections/882635250203/</a> and <a href="https://imaps.goodwright.com/collections/340215254997/">https://imaps.goodwright.com/collections/340215254997/</a> for LIN28A and PABPC1/4 iCLIPs, respectively); and on the updated Flow webserver (see <a href="https://app.flow.bio/projects/882635250203/">https://app.flow.bio/projects/882635250203/</a> and <a href="https://app.flow.bio/projects/340215254997/">https://app.flow.bio/projects/340215254997/ </a>for LIN28A and PABPC1/4 iCLIPs, respectively).</p> <h2>Downstream computational analysis of enclosed data</h2> <p>The code, used to analyse the data enclosed here and train the CNN to predict transcript stability in naive-to-primed transition based on 3'UTR nucleotide sequence, is available at GitHub (<a href="https://github.com/ulelab/LIN28A_RNPreassembly_bioinformatics">https://github.com/ulelab/LIN28A_RNPreassembly_bioinformatics</a>) and archived on Zenodo (<a href="../doi/10.5281/zenodo.10054297">https://zenodo.org/doi/10.5281/zenodo.10054297</a><strong>).</strong></p>
UPF3A and UPF3B are redundant and modular activators of nonsense-mediated mRNA decay in human cells
<p>Source data for the publication: UPF3A and UPF3B are redundant and modular activators of nonsense-mediated mRNA decay in human cells.<br> Includes raw image data (e.g. agarose gels, western blots, northern blots), quantifications, qPCR raw Ct values and other supporting material.</p>
YB1 dephosphorylation attenuates atherosclerosis by promoting CCL2 mRNA decay
<p> Y-box binding protein 1 (YB1) is an RNA binding protein (RBP) that has been reported to play important roles in inflammation and atherosclerotic plaque formation. To explore the molecular mechanism of phosphorylated YB1 (pYB1) in atherosclerosis <em>in vitro</em>, we constructed YB1 phosphorylation site (Ser-100) mutant stable smooth muscle cell line (3ds-V5) and performed RNA profile screening through RNA-seq. We found inflammatory pathways and CCL2 was significantly decreased in the 3dS-V5 YB1 mutant compared with the control group (YB1-V5).</p>
Data from: Nonsense-mediated decay of alternative pre-mRNA splicing variants is a major determinant of the Arabidopsis steady state transcriptome
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Transcriptome Analysis Reveals Extensive Alternative Splicing-Coupled Nonsense-Mediated mRNA Decay in a Human Cell Line
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Polysome fractionation analysis reveals features important for human nonsense-mediated mRNA decay
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Differential Gene Expression and mRNA decay in Wild-Type and Myeloid-specific TTP Knock-out macrophages using RNA-Seq
GEO Series GSE229922. Mus musculus. 64 samples. Type: Expression profiling by high throughput sequencing.
Oligodendrocyte differentiation alters tRNA modifications and codon-dependent mRNA decay [QuantM-seq II]
GEO Series GSE198271. Saccharomyces cerevisiae. 8 samples. Type: Non-coding RNA profiling by high throughput sequencing.
Global analysis of Upf1 in mESCs reveals expanded scope of nonsense-mediated mRNA decay
GEO Series GSE41785. Mus musculus. 23 samples. Type: Expression profiling by high throughput sequencing; Other.
m6A sites in the coding region trigger translation-dependent mRNA decay (SLAM-seq)
GEO Series GSE273217. Homo sapiens. 18 samples. Type: Expression profiling by high throughput sequencing.
Embryonic lumenogenesis is controlled by selective mRNA decay triggered by LIN28A relocation [Slam-Seq]
GEO Series GSE169554. Mus musculus. 90 samples. Type: Expression profiling by high throughput sequencing.
m6A is decoded by modified tRNAs to coordinate mRNA decay [SLAM-Seq]
GEO Series GSE247664. Homo sapiens. 18 samples. Type: Expression profiling by high throughput sequencing; Other.
Knockdown of YBX1 impairs alternative splicing and maternal mRNA decay during pre-implantation development
GEO Series GSE182908. Capra hircus. 6 samples. Type: Expression profiling by high throughput sequencing.
Heritable variation of mRNA decay rates in yeast
GEO Series GSE60617. Saccharomyces cerevisiae. 18 samples. Type: Expression profiling by high throughput sequencing.
Whole genome analysis of mRNA decay in P. falciparum reveals a lengthening of mRNA half-life during the IDC
GEO Series GSE8099. Plasmodium falciparum; Saccharomyces cerevisiae. 104 samples. Type: Expression profiling by array.
m6A is decoded by modified tRNAs to coordinate mRNA decay [Quant-seq]
GEO Series GSE291842. Homo sapiens. 18 samples. Type: Expression profiling by high throughput sequencing.
m6A is decoded by modified tRNAs to coordinate mRNA decay [miCLIP]
GEO Series GSE248112. Homo sapiens. 1 samples. Type: Other.
A novel Smg6 mouse model reveals circadian clock regulation through the nonsense-mediated mRNA decay pathway
GEO Series GSE208769. Mus musculus. 52 samples. Type: Expression profiling by high throughput sequencing.
Oligodendrocyte differentiation alters tRNA modifications and codon-dependent mRNA decay [DecaySeq]
GEO Series GSE182809. Mus musculus. 26 samples. Type: Expression profiling by high throughput sequencing.
Translation of zinc finger domains induces ribosome collision and Znf598-dependent mRNA decay in zebrafish [Ribo-seq]
GEO Series GSE236144. Danio rerio. 4 samples. Type: Other; Expression profiling by high throughput sequencing.
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