Project description:To study the function of zebrafish Ybx1 during early embryogenesis, we generated maternal ybx1 (Mybx1) mutant using CRISPR/Cas9 and report the transcriptome-wide changes in comparison to wild-type (WT) embryos. Our analysis reveals a dramatic loss of maternal mRNA decay and zygotic genome activation in Mybx1 embryos during maternal-to-zygotic transition.

2018-09-01 | GSE108924 | GEO

Binding in wild type embryos: SoxN.

Project description:Genome-wide binding of SoxN in wild type embryos: SoxNDam (DamID, stage 8-11), SoxND1 (ChIP, stage 8-11), SoxND2 (ChIP, stage 8-11), SoxNPA179 Early (ChIP, stage 7-10), and SoxNPA179 Late (ChIP, stage 11-13).

2014-04-23 | GSE47337 | GEO

Small and long RNAs profiling of testis, developing oocytes and early embryos wild-type and Pld6-deficient golden hamster

Project description:Small and long RNAs profiling of developing oocytes and early embryos in wild-type and Pld6-deficient golden hamster females, as well as profiling of testis of wild-types and Pld6-mutents

2022-02-03 | GSE195935 | GEO

Nucleosome occupancy of C. elegans wild-type (N2) early stage embryos vs. mature sperm from him-8(e1489) males

Project description:To determine how the genome is packaged in C. elegans sperm, we isolated adult him-8(e1489) males and collected mature sperm (~99% purity). We utilized micrococcal nuclease digestion followed by paired-end sequencing (MNase-seq) to evaluate the presence of nucleosomes across the genome in sperm vs. early embryos. We found that the sperm genome retains nucleosomes genome-wide, comparable to wild-type early embryos.

2018-07-23 | GSE115705 | GEO

Transcript profiling of wild-type and dcl1-5 early globular embryos

Project description:DICER-LIKE1 (DCL1) is required for miRNA biogenesis and embryonic pattern formation. Presumably the patterning defects observed in dcl1-5 null embryos are due to the loss of miRNAs and the consequent up-regulation of their respective targets. To test which miRNA targets were up-regulated in dcl1 embryos relative to wild-type embryos, we performed genome-wide transcript profiling of wild-type and dcl1-5 early globular embryos using directional mRNA-Seq. For RNA isolation, pools of 30 Col-0 (wild-type) and dcl1-5 early globular embryos were hand-dissected in water, immediately transferred to 30 ul of RNAlater (Ambion), incubated at 60M-BM-0 C with 500 ul TRIzol Reagent (Invitrogen) for 30 minutes, and then purified according to the TRIzol Reagent protocol for RNA isolation from small quantities of tissue (Invitrogen). Two rounds of linear amplification of poly(A) RNA were performed using the Arcturus RiboAmp HS Plus kit (Molecular Devices). Strand-specific mRNA-Seq libraries were generated as previously described (Guo et al., Nature, 2010). After removing adaptor sequences, sequences were mapped to the Arabidopsis thaliana genome (TAIR9 assembly) using the Bowtie short read aligner allowing up to two mismatches within a 25 nt M-bM-^@M-^XseedM-bM-^@M-^Y sequence and retaining reads mapping uniquely to the genome. Since the Arcuturus RiboAmp HS Plus kit generates amplified RNAs in the antisense orientation, reads were counted as matching TAIR9 annotated genes if they overlapped the antisense strand.

2010-12-01 | E-GEOD-25404 | biostudies-arrayexpress

Transcriptome analysis of wild-type and maternal zygotic double mutant of nup85;nup133 zebrafish embryos during early development

Project description:To study the function of zebrafish nuclear pores during early embryogenesis, we generated maternal zygotic double mutant of nup85;nup133 (MZnup85;nup133) using CRISPR/Cas9 and report the transcriptome-wide changes in comparison to wild-type (WT) embryos. Our analysis reveals a dramatic delay of maternal mRNA degradation and zygotic genome activation in MZnup85;nup133 embryos during maternal-to-zygotic transition.

2023-03-04 | GSE146394 | GEO

zebrafish embryos proteome for slbp2 KO F3 and wild type

Project description:zebrafish embryos proteome for slbp2 KO F3 and wild type at 2.5hpf and 3.5hpf, three replicates for every sample. There are 12 samples in total. Then we analyse the different expressed genes and hope to find out clue which result in serious phenotype of slbp2 KO F3.

2018-11-27 | PXD008614 | Pride

Expression data of wild-type and dcl1-15 torpedo-staged embryos

Project description:Severe loss-of-function alleles of DCL1 are embryonic lethal. Defects in cell division were seen as early as the globular stage in the strong loss-of-function allele dcl1-15. Phenotypic work with dcl1-15 and the null allele dcl1-5 suggested that, in addition to the severe patterning defects, the mutants were maturing earlier than wild-type embryos. We performed global gene expression analysis of dcl1-15 and wild-type torpedo staged embryos to examine this maturation phenotype further. The results suggested that DCL1 is a heterochronic gene. Comparisons to a time series of embryo development (http://www.seedgenenetwork.net/arabidopsis) showed that the genes differentially expressed in dcl1-15 embryos behaved more like green-cotyledon stage embryos than torpedo embryos.

2011-02-17 | GSE24887 | GEO

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