run_metadata: 51438
This data as json
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| 51438 | SRR8787637 | SRX5577571 | SRS4539474 | SRP189499 | PRJNA529224 | Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: iCLIP | PRJNA529224 | Other | Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT thousands of maternal transcripts are regulated however how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay we identified cis regulatory sequences in the three prime UTR including poly U motifs that are associated with mRNA stability. In contrast miR 430 target sequences UAUUUAUU AU rich elements ARE CCUC and CUGC elements emerged as destabilizing motifs with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the iCLIP part of the study. | Raw multiplex: iCLIP zff9 B1;iCLIP org B1;iCLIP srsf4 B1;iCLIP hnrnpa0a B1 | Raw multiplex: iC zff9 B1 AGN001179;iC org B1 AGN001180;iC srsf4 B1 AGN001181;iC hnrnpa0a B1 AGN001182 | strain:TU/AB|age:4|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:FLAG antibody|sample ref:AGS001023;AGS001024;AGS001025;AGS001026|replicate ref:AGN001179;AGN001180;AGN001181;AGN001182|replicate order:1|barcode:CACA;AGAG;TCTC;GTGT|BioSampleModel:Model organism or animal | Raw multiplex: iCLIP zff9 B1;iCLIP org B1;iCLIP srsf4 B1;iCLIP hnrnpa0a B1 | AGR001616;AGR001624;AGR001626;AGR001628 | AGR001616;AGR001624;AGR001626;AGR001628 | RNA | OTHER | TRANSCRIPTOMIC | unspecified | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP189499 | C78TPACXX_A_001_R1.fastq.gz | fastq | 10301944248.0 | 135551898.0 | C78TPACXX A 001 R1.fastq.gz | 0:76 | A:3081993818;C:2552332073;G:2597278544;T:2069986979;N:352834 | 76 | 3081993818 | 2552332073 | 2597278544 | 2069986979 | 352834 | SRX5577571 | SRS4539474 | SRA866141 | Yale_Giraldez|Genetics | Yale_Giraldez_Group | 1 | 0.00026 | 0.00011 | 0.99953 | 0.55555 | 76 | T | under 1.2% mapping rate | illumina | hiseq_era | unknown | unknown | unknown | bulk | clip | iclip | United States | 2019-05-31 | Blastula | Embryo | Embryo Imprecise | All anatomical structures |