run_metadata: 51445
This data as json
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| 51445 | SRR8787644 | SRX5577564 | SRS4539469 | 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. | iCLIP iCLIP hrnpd B4 | iCLIP iC hrnpd B4 AGN001326 | strain:TU/AB|age:4|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:FLAG antibody|sample ref:AGS001030|replicate ref:AGN001326|replicate order:4|barcode:TCTC|BioSampleModel:Model organism or animal | iCLIP iCLIP hrnpd B4 | AGR001659 | AGR001659 | RNA | OTHER | TRANSCRIPTOMIC | unspecified | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP189499 | AGR001659_R1.fastq.gz | fastq | 401606803.0 | 13049141.0 | AGR001659 R1.fastq.gz | 0:30.78 1:0 | A:120013041;C:76269300;G:84288752;T:121032164;N:3546 | 30 | 0 | 120013041 | 76269300 | 84288752 | 121032164 | 3546 | SRX5577564 | SRS4539469 | SRA866141 | Yale_Giraldez|Genetics | Yale_Giraldez_Group | 1 | 0.42881 | 0.32719 | 0.85366 | 0.58367 | 20 | B | usable mapping rate | illumina | hiseq_era | unknown | unknown | unknown | bulk | clip | iclip | United States | 2019-05-31 | Blastula | Embryo | Embryo Imprecise | All anatomical structures |