run_metadata: 56029
This data as json
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| 56029 | SRR10836788 | SRX7508633 | SRS5949025 | SRP239626 | PRJNA599208 | Genome wide localization of RNAs during early zebrafish development | GSE143208 | Transcriptome Analysis | We employed transcriptomics methods to examine RNAs from the nuclear and cytosolic fractions from zebrafish embryos at different stages of development. The RNA seq revealed spatial and temporal regulation of lncRNA expression during zebrafish development. Overall design: Localization of RNAs in the nuclear and cytosolic fractions of zebrafish embryonic cells in the 64 Cell 256 Cell 1000 Cell Dome and Shield stages of development. | pubmed:33795334 | Dome Nuc | GSM4252154 | source name:Dome stage embryo|tissue:zebrafish embryos|developmental stage:Dome|fraction:Nuclear | Dome Nuc | RNA seq reads were trimmed using the Trimmomatic v0.27 and then mapped to the Zv9 genome using STAR v2.6.0a with parameters p8 Transcript per million TPM was calculated using the Stringtie and Ballgown program Genome build: Zv9 Supplementary files format and content: tab delimited TPM files for all stages | Dome stage embryo | Dechorionated embryos were then washed twice with 1 X PBS Phosphate buffer solution ThermoFisher. RLN buffer was added to the tube containing embryos and the yolk sac disrupted releasing the cells in the buffer. This was then incubated on ice for 5 mins and centrifuged. The resulting supernatant was collected and labelled as the cytosolic fraction. The pellet was washed twice with 200 µL of RLN buffer and finally collected and labelled as the nuclear fraction. | RNA was extracted using the Rneasy mini kit Sequencing libraries were prepared using the TruSeq Stranded Total RNA library Prep kit with the Illumina Ribo Zero rRNA removal kit Human Mouse Rat. | Wild type male and female zebrafish AB strain were set up in breeding tanks overnight and the eggs were collected the next day as soon as 10 min they were laid important to get synchronised embryos. About 100 500 depending upon the stage embryos were collected for each developmental stage 64 cell 256 cell 1000 cell shield 24hpf 50hpf. The embryos were treated with Pronase protease from Streptomyces griseus Sigma Aldrich to remove the chorion 1mL of Pronase working solution 1mg/mL was added to 2 3 ml of fish water containing embryos. | tissue:zebrafish embryos|developmental stage:Dome|fraction:Nuclear | GSM4252154 | GSM4252154: Dome Nuc; Danio rerio; RNA Seq | GSM4252154 | 1 | RNA was extracted using the Rneasy mini kit Sequencing libraries were prepared using the TruSeq Stranded Total RNA library Prep kit with the Illumina Ribo Zero rRNA removal kit Human Mouse Rat. | GEO Accession:GSM4252154 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP239626 | Dome-N2_L001_R1_001.fastq.gz Dome-N2_L001_R2_001.fastq.gz | fastq fastq | 2074718856.0 | 13753362.0 | GSM4252154 r1 | 0:75.47 1:75.38 | A:548207869;C:474119517;G:498330967;T:553614124;N:446379 | 75 | 75 | 548207869 | 474119517 | 498330967 | 553614124 | 446379 | SRX7508633 | SRS5949025 | SRA1020776 | GEO | School of Biosciences, University of Birmingham | 2 | 0.92904 | 0.93027 | 0.25794 | 0.25635 | 0.73314 | 0.73543 | 0.63799 | 0.63772 | 76 | 75 | B | B | biological fallback assumption | illumina | nextseq | unknown | rrna_depletion | ribozero | bulk | bulk | bulk | United Kingdom | 2020-01-06 | Blastula | Embryo | Embryo Imprecise | All anatomical structures |