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Methods for normalization of RNA-sequencing gene expression data commonly assume equal total expression between compared samples. In contrast, scenarios of global gene expression shifts are many and increasing. Here we compare the performance of three normalization methods when polyA(+) RNA content fluctuates significantly during zebrafish early(More)
The merging of the maternal and paternal genomes into a single pronucleus after fertilization is accompanied by a remarkable reconfiguration of chromatin in the newly formed zygote. The first stages of embryonic chromatin remodeling take place in the absence of ongoing transcription, during a species-specific developmental time-frame. Once(More)
Fertilization is followed by complex changes in cytoplasmic composition and extensive chromatin reprogramming which results in the abundant activation of totipotent embryonic genome at embryonic genome activation (EGA). While chromatin reprogramming has been widely studied in several species, only a handful of reports characterize changing transcriptome(More)
Zebrafish embryos are transcriptionally silent until activation of the zygotic genome during the 10th cell cycle. Onset of transcription is followed by cellular and morphological changes involving cell speciation and gastrulation. Previous genome-wide surveys of transcriptional changes only assessed gene expression levels; however, recent studies have shown(More)
BACKGROUND Somatic copy number alterations (SCNAs) occurring in tumors can provide information about tumor classification, patient's outcome or treatment targets. Liquid biopsies, incl. plasma samples containing circulating cell-free tumor DNA (ccfDNA) can be used to assess SCNAs for clinical purposes, however specify and reliability of methods have to be(More)
Common features of embryonic genome activation in mammalian and non-mammalian embryos are the colocalization of pre-assembled complexes of maternally inherited nucleolar proteins, the so-called nucleolus precursor bodies and de novo synthesized transcripts with ribosomal DNA. The de novo transcription of messenger RNA and ribosomal RNA proteins is required(More)
These results suggest that wge is involved in epigenetic regulation , but its function is different from typical PcG and trxG. In this study, to know whether wge maintains either silenced or active transcriptional states, we investigated the effects of wge mutation on PcG / trxG PcG/trxG response element (PRE / TRE)– mediated (PRE/TRE)-mediated gene(More)
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