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The mRNA-Seq data of human-Zic3 overexpression in chicken limbs

ABSTRACT: The mRNA-Seq data of human-Zic3 overexpression in chicken limbs

PROVIDER: PRJNA1106851 | ENA |

REPOSITORIES: ENA

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The mRNA-Seq data of Zic3 overexpression in chicken limbs

Project description:The mRNA-Seq data of Zic3 overexpression in chicken limbs

| PRJNA1186557 | ENA

The mRNA-Seq data of human-Zic3 overexpression in chicken limbs

Project description:We observed Zic3 highly expressed in the anterior regions of limb buds in all investigated tetrapods. To investigate the function of the Zic3 in limbs, we overexpressed the human-Zic3 gene in the lateral plate mesoderm (LPM) of developing chicken hindlimbs at HH10 using the RCAS avian retrovirus. Subsequently, the embryos were allowed to incubate until HH30. Autopod and zeugopod regions were dissected and subjected to transcriptome sequencing (mRNA-Seq), with the corresponding positions from individuals injected with the empty RCAS vector serving as controls. The results of the differential analysis and enrichment analysis revealed the regulatory network of Zic3 and various regulatory pathways that may be affected.

2025-08-27 | GSE266376 | GEO

The mRNA-Seq data of Zic3 overexpression in chicken limbs

Project description:Birds exhibit a remarkable diversity in limb morphology. Zic3, a transcription factor highly expressed in the anterior of the limb, has differential expression among bird species. To study how it regulates digit morphogenesis in birds, we overexpressed the chicken-Zic3 gene in the lateral plate mesoderm (LPM) of developing chicken hindlimbs at Hamburger Hamilton (HH) stage 10 using the RCAS avian retrovirus. At HH30, the autopod was dissected and subjected to transcriptome sequencing (mRNA-Seq), with the corresponding positions of individuals injected with the empty RCAS vector serving as controls. Enrichment analysis of differential genes and GSEA analysis suggest that the Zic3 gene inhibits multiple pathways related to skeletal development, resulting in a delay in digit development.

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Zic3 interacts with distant regulatory elements to regulate zebrafish developmental genes

Project description:Zic3 regulates early embryonic patterning in vertebrates. Its loss-of-function disrupts gastrulation, left-right patterning, and neurogenesis. We use the zebrafish as a model to study the developmental role of Zic3 in vivo. Using a combination of two genomics approaches – ChIP-seq and microarray, we identified Zic3 targets, which include genes from the Nodal and Wnt pathways, and show for the first time cis-regulation of these genes by Zic3 using in vivo enhancer assay. We uncovered a previously unrecognized link between Zic3 and the non-canonical Wnt pathway in gastrulation and left-right patterning, and identified neural pre-pattern genes as Zic3 targets during the early steps of neural induction. Zic3 preferably binds to distal intergenic regions, some of which contain evolutionarily conserved functional enhancers. Our study establishes the zebrafish as an excellent model for genome-wide study of a transcription factor in vivo.

2014-02-27 | GSE41458 | GEO

Zic3 interacts with distant regulatory elements to regulate zebrafish developmental genes

2014-02-27 | E-GEOD-41458 | biostudies-arrayexpress

Zic3 ChIP-on-chip in mouse ES cells

Project description:The transcription factor Zic3 is required for maintenance of embryonic stem (ES) cell pluripotency (Lim LS et al, Mol Biol Cell. 2007;18:1348-1358). By genome-wide chromatin immunoprecipitation (ChIP-chip) in ES cells, we have identified 379 direct Zic3 targets, many of which are functionally associated with pluripotency, cell cycle, proliferation, oncogenesis and early embryogenesis.

2010-09-13 | GSE22195 | GEO

ZIC2 and ZIC3 promote SWI/SNF recruitment to safeguard progression towards human primed pluripotency [ATAC-Seq]

Project description:ZIC2 and ZIC3 are essential for acquisition and maintenance of primed pluripotency. In this study, we conducted ATAC-seq in single and compound knockout of ZIC2, ZIC3 and ZIC5 primed hESCs, naïve hESCs lacking ZIC3 that inducibly express ZIC2, naive hESCs that inducible express ZIC2 or ZIC3, ZIC3-depleted primed hESCs that were cultured in 5iLAF medium for six days and undergoing reversion to a naive state, naive hESCs expressing ectopic ZIC2 in the presence of a BRG1 PROTAC.

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Single cell transcriptomes of developing chicken hind limbs at stages HH25, HH29 and HH31

Project description:Single cell transcriptomes of developing chicken hind limbs at stages HH25, HH29 and HH31

| PRJNA540263 | ENA

Single cell transcriptomes of developing chicken hind limbs at stages HH21, HH24 and HH27

Project description:Single cell transcriptomes of developing chicken hind limbs at stages HH21, HH24 and HH27

| PRJNA730553 | ENA

PLURIPOTENCY REGULATOR ZIC3 IS AN EARLY LINEAGE SPECIFIER

Project description:Sustained expression of the key pluripotency transcriptional regulators and proliferative factors is needed for the maintenance of embryonic stem cells and early progenitors of various lineages. Zic3 is one of those factors which has been shown to be important for embryonic stem cell pluripotency. Through combinatorial analysis of transcription factor binding sites and the corresponding gene-regulation, we show that Zic3 not only activates key pluripotency genes but also acts cooperatively with them in connecting important circuits of regulation in ES cell in proliferation and maintenance of early progenitors.

2015-12-30 | GSE37889 | GEO

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