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SRX5587877: GSM3689553: PGC_7hpf_RNA-seq_rep1_RUN2; Danio rerio; RNA-Seq
1 ILLUMINA (Illumina NovaSeq 6000) run: 109.1M spots, 22G bases, 6.5Gb downloads

Submitted by: NCBI (GEO)
Study: Retention of paternal epigenetic memory in the developing teleost germline [alt-splicing]
show Abstracthide Abstract
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: In order to perform alternative splicing analysis, PGC 7 hpf, PGC 24 hpf, Soma 7 hpf and Soma 24 hpf low-input RNA-seq samples have been sequenced on an additional lane of Nova-seq 6000 and analyzed together with the previous RNA-seq run (GSE122480).
Sample: PGC_7hpf_RNA-seq_rep1_RUN2
SAMN11280447 • SRS4549124 • All experiments • All runs
Organism: Danio rerio
Instrument: Illumina NovaSeq 6000
Strategy: RNA-Seq
Selection: cDNA
Layout: PAIRED
Construction protocol: 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)
Experiment attributes:
GEO Accession: GSM3689553
Runs: 1 run, 109.1M spots, 22G bases, 6.5Gb
Run# of Spots# of BasesSizePublished


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