run_metadata: 50624
This data as json
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| 50624 | SRR8182168 | SRX5002135 | SRS4036798 | SRP168473 | PRJNA505329 | Retention of paternal epigenetic memory in the developing teleost germline [RNA Seq] | GSE122480 | Transcriptome Analysis | Two waves of DNA methylation reprogramming occur during mammalian embryogenesis; during preimplantation development and during primordial germ cell PGC formation. However it is currently unclear how evolutionarily conserved these processes are. Here we characterize the DNA methylomes of zebrafish PGCs at four developmental stages and unravel retention of paternal epigenetic memory in stark contrast with the findings in mammals. Gene expression profiling of zebrafish PGCs at same developmental stages revealed that the embryonic germline is defined by a small number of markers that display strong developmental stage specificity and that are uncoupled from DNA methylation mediated regulation. Overall design: Using low input RNA seq we have profiled transcriptomes of zebrafish primordial germ cells PGCs and age matched somatic cells at 4 blastula 7 gastrula 24 pharyngula prim 5 and 36 pharyngula prim 25 hpf | parent bioproject:PRJNA506076 | pubmed:31296860 | PGC 36hpf RNA seq rep2 | GSM3467118 | tissue:PGCs 36hpf RNA seq replicate 2|cell type:primordial germ cells|developmental stage:36hpf | PGC 36hpf RNA seq rep2 | Adaptor sequences and low quality bases were removed using TrimGalore https://github.com/FelixKrueger/TrimGalore/ Sequencing reads were aligned to zebrafish genome danRer10 using STAR Dobin et al 2013; Bioinformatics Transcript abundancies were quantified using RSEM tool Li et al 2011 BMC Bioinformatics Differential gene expression analysis was performed using edgeR Robinson et al 2010; Bioinformatics; McCarthy et al 2012; Nucleic Acids Research Genome build: danRer10 Supplementary files format and content: .csv format containing transcripts per million TPM; expected count and effective length for PGCs and Soma RNA seq samples at 4 developmental stages in replicates. | PGCs 36hpf RNA seq replicate 2 | PGCs were FACS sorted from the kop EGFP F nos3’UTR transgenic zebrafish line Library prep was performed using Clontech SMARTer pico mammalian v2 kit and sequenced on NovaSeq 6000 2x100bp | cell type:primordial germ cells|developmental stage:36hpf | GSM3467118 | GSM3467118: PGC 36hpf RNA seq rep2; Danio rerio; RNA Seq | GSM3467118 | 1 | PGCs were FACS sorted from the kop EGFP F nosthree primeUTR transgenic zebrafish line Library prep was performed using Clontech SMARTer pico mammalian v2 kit and sequenced on NovaSeq 6000 2x100bp | GEO Accession:GSM3467118 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP168473 | PGC_36h_rep2_R1.fastq.gz PGC_36h_rep2_R2.fastq.gz | fastq fastq | 9702849214.0 | 48033907.0 | GSM3467118 r1 | 0:101 1:101 | A:1957602439;C:2881656243;G:2916349837;T:1946652829;N:587866 | 101 | 101 | 1957602439 | 2881656243 | 2916349837 | 1946652829 | 587866 | SRX5002135 | SRS4036798 | SRA808716 | GEO | Developmental Epigenomics, Genomics and Epigenetics, Garvan Institute | 2 | 0.95843 | 0.95704 | 0.25621 | 0.23569 | 0.7666 | 0.76926 | 0.78788 | 0.83187 | 101 | 101 | B | B | biological fallback assumption | illumina | novaseq_era | full_length | cdna_unspecified | smarter | bulk | unknown | unknown | Australia | 2018-11-13 | Pharyngula | Embryo | Gonad | Reproductive System |