run_metadata: 55454
This data as json
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| 55454 | SRR10436029 | SRX7131789 | SRS5640785 | SRP229649 | PRJNA588137 | rnf213a knockout zebrafish Transcriptome or Gene expression | PRJNA588137 | Transcriptome Analysis | To explore the downstream molecules of rnf213a we conducted transcriptome sequencing to detect differentially expressed genes DEGs between +2bp rnf213a / mutant and wild type zebrafish at 72hpf and 120hpf. | normal 72hpf | strain:wild type|dev stage:72hpf|sex:pooled male and female|tissue:whole mount embryos|BioSampleModel:Model organism or animal | RNA Seq of Danio rerio: whole mount embryos | rnf213a 1 | rnf213a 1 | The polyA mRNA isolation was performed using NEBNext PolyA mRNA Magnetic Isolation Module NEB or Ribo Zero rRNA removal Kit illumina. The mRNA fragmentation and priming was performed using NEBNext First Strand Synthesis Reaction Buffer and NEBNext Random Primers. First strand cDNA was synthesized using ProtoScript II Reverse Transcriptase and the second strand cDNA was synthesized using Second Strand Synthesis Enzyme Mix. The purified double stranded cDNAby AxyPrep Mag PCR Clean up Axygenwas then treated with End Prep Enzyme Mix to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using AxyPrep Mag PCR Clean up Axygen and fragments of 360 bp with the approximate insert size of 300 bp were recovered. Each sample was then amplified by PCR for 11 cycles using P5 and P7 primers with both primers carrying sequences which can anneal with flow cell to perform bridge PCR and P7 primer carrying a six base index allowing for multiplexing. The PCR products were cleaned up using AxyPrep Mag PCR Clean up Axygen validated using an Agilent 2100 Bioanalyzer Agilent Technologies Palo Alto CA USA and quantified by Qubit 2.0 Fluorometer Invitrogen Carlsbad CA USA. | RNA-Seq | TRANSCRIPTOMIC | RANDOM | SINGLE | ILLUMINA | HiSeq X Ten | SRP229649 | rnf213a_1 | fastq | 3592044900.0 | 23946966.0 | rnf213a 1.gz | 0:150 1:0 | A:952165099;C:842448366;G:843305876;T:953891694;N:233865 | 150 | 0 | 952165099 | 842448366 | 843305876 | 953891694 | 233865 | SRX7131789 | SRS5640785 | SRA993760 | First affiliated hospital of Sun Yat-sen university|neurology | First affiliated hospital of Sun Yat-sen university | 1 | 0.93128 | 0.09035 | 0.65445 | 0.47792 | 150 | B | usable mapping rate | illumina | hiseq_era | unknown | random_priming | nebnext | bulk | unknown | unknown | China | 2019-11-13 | Larval | Larval | Embryo Imprecise | All anatomical structures |