{"database": "metadata", "table": "run_metadata", "rows": [[64243, "SRR14362886", "SRX10715472", "SRS8805906", "SRP317900", "PRJNA726251", "Ribosome profiling analysis of zebrafish embryos injected with the codon tag reporter library", "GSE173604", "Other", "We measured the effect of codons on mRNA stability in zebrafish embryos using reporter mRNAs. We showed that slow decoding of codons by the ribosome promoted mRNA degradation in zebrafish. Overall design: Ribosome profiling of zebrafish embryos.", null, null, null, "zebrafish monosome codontag rep2", "GSM5272498", null, "source name:whole embryo|strain:AB|tissue:whole embryo|treatment:PACE library injected", "zebrafish monosome codontag rep2", "Library strategy: Ribo seq Basecalling with Illumina Casava 1.8 software. three prime adapter trimming with Fastp toolkit. Library sorting based on sample barcode sequence and random barcode trimming with custom script. rRNA and other non coding RNA alignment with bowtie2 v2.4.1. Alignment with TopHat v2.1.1. Read quantitation using custom scripts. Genome build: GRCz11 Supplementary files format and content: *.txt: Tab delimited text files contain five columns: 1. transcript name; 2. from 5end of the transcript nt used for read counting; 3. from start codon of the transcript nt used for read counting; 4. codon; 5. read count.", "whole embryo", "PACE reporter mRNA library was injected at 1 cell stage.", "Fifty to sixty zebrafish embryos injected with PACE reporter mRNAs were snap frozen at the sphere stage and lysed with lysis buffer containing cycloheximide. RNA extraction  preadenylated linker ligation  rRNA depletion  reverse transcription  cDNA circularization  PCR amplification for ribosome profiling.", "Fertilized eggs were obtained by natural breedings.", "strain:AB|tissue:whole embryo|treatment:PACE library injected", "GSM5272498", "GSM5272498: zebrafish monosome codontag rep2; Danio rerio; OTHER", "GSM5272498", null, "1", "Fifty to sixty zebrafish embryos injected with PACE reporter mRNAs were snap frozen at the sphere stage and lysed with lysis buffer containing cycloheximide. 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