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Differences in gene expression patterns in mouse embryonic fibroblast Flp-In-3T3 cell lines stably expressing Pax6 or Pax6(5a).

ABSTRACT: Novel target genes for the two transcription factor isoforms Pax6 and Pax6(5a) were identified by generating mouse embryonic fibroblast cell lines stably expressing either Pax6 or Pax6(5a), and comparing their gene expression pattern with the original mouse embryonic fibroblast cell line.

ORGANISM(S): Mus musculus

PROVIDER: GSE31402 | GEO | 2012/03/22

SECONDARY ACCESSION(S): PRJNA145725

REPOSITORIES: GEO

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Differences in gene expression patterns in mouse embryonic fibroblast Flp-In-3T3 cell lines stably expressing Pax6 or Pax6(5a).

Project description:Novel target genes for the two transcription factor isoforms Pax6 and Pax6(5a) were identified by generating mouse embryonic fibroblast cell lines stably expressing either Pax6 or Pax6(5a), and comparing their gene expression pattern with the original mouse embryonic fibroblast cell line. Flp-In-3T3 cell lines were generated according to the manufacturers instruction (Invitrogen), using the mouse Pax6 and Pax6(5a) cDNA as insert. Correct inserts were verified by PCR, sequencing and Westernblot.

2012-03-22 | E-GEOD-31402 | biostudies-arrayexpress

3T3 cell lines stably expressing Pax6 or Pax6(5a)--a new tool used for identification of common and isoform specific target genes.

Project description: Not available

| S-EPMC3285655 | biostudies-literature

Pax6 regulates the expression of Dkk3 in murine and human cell lines, and altered responses to Wnt signaling are shown in FlpIn-3T3 cells stably expressing either the Pax6 or the Pax6(5a) isoform.

Project description: Not available

| S-EPMC4100929 | biostudies-literature

Pax6 mutant neocortex vs. wild type

Project description:Pax6 is a transcription factor with key functional roles in embryonic development. In order to identify downstream effectors of Pax6 in the developing cerebral cortex we performed microarray analysis. We compared gene expression profiles of cortical tissues isolated from wild type and Pax6-/- mouse embryos. In order to identify Pax6 downstream targets we carried out microarray analysis of Pax6-/- mutant mice. Pax6 is highly expressed in the mouse cerebral cortex at embryonic day E14.5, therefore we selected this tissue in order to compare gene expression profiles between wild type and Pax6-/- homozygous cortici. RNA samples were isolated from three mutant and three wild type embryos.

2011-10-31 | E-GEOD-32271 | biostudies-arrayexpress

Agrobacterium tumefaciens 5A strain:5A

Project description:Agrobacterium tumefaciens 5A strain:5A Genome sequencing and assembly

| PRJNA75079 | ENA

Pax6 mutant neocortex vs. wild type

2011-10-31 | GSE32271 | GEO

Identification of in vivo DNA-binding mechanisms of Pax6 and reconstruction of Pax6-dependent gene regulatory networks during lens and forebrain development

Project description:The transcription factor Pax6 is comprised of the paired domain (PD) and homeodomain (HD). In the developing forebrain, Pax6 is expressed in ventricular zone precursor cells and in specific subpopulations of neurons; absence of Pax6 results in disrupted cell proliferation and cell fate specification. Pax6 also regulates the entire lens developmental program. To reconstruct Pax6-dependent gene regulatory networks (GRNs), ChIP-seq studies were performed using lens and forebrain chromatin from mice. A total of 3,723 (forebrain) and 3,514 (lens) Pax6-containing peaks were identified, with ~70% of them found in both tissues and thereafter called “common” peaks. Analysis of Pax6-bound peaks identified motifs that closely resemble Pax6-PD, -PD/HD and -HD established binding sequences. Mapping of H3K4me1, H3K4me3, H3K27ac, H3K27me3 and RNA polymerase II revealed distinct types of tissue-specific enhancers bound by Pax6. Pax6 directly regulates cortical neurogenesis through activation (e.g. Dmrta1 and Ngn2) and repression (e.g. Ascl1, Fezf2, and Gsx2) of transcription factors. In lens, Pax6 directly regulates cell cycle exit control via components of FGF (Fgfr2, Ccnd1, and Prox1) and Wnt (Dkk3, Wnt7a, Lrp6, Bcl9l, and Ccnd1) signaling pathways. Collectively, these studies provide genome-wide analysis of Pax6-dependent GRNs in lens and forebrain and establish novel roles of Pax6 in organogenesis. Examination of Pax6 in mouse embryonic forebrain and newborn lens. We performed ChIP-seq on mouse E12.5 embryonic forebrain and newborn lens. Genome-wide binding sites of Pax6, H3K4me1, H3K4me3, H3K27ac, H3K27me3, and Pol2 were generated. We also performed RNA-seq on mouse E12.5 embryonic forebrain and newborn lens epithelial cells and fibers.

2015-07-09 | E-GEOD-66961 | biostudies-arrayexpress

Shigella flexneri 5a

Project description:Shigella flexneri 5a

| PRJNA16047 | ENA

Toxoplasma gondii eIF-5A knockdown iTraq

Project description:Proliferative stage (tachyzoite) is a critical factor in the transmission and pathogenesis of Toxoplasma gondii (T. gondii), which is capable of infecting a large variety of host cells. Proto-oncogene eukaryotic translation initiation factor (eIF-5A) is thought to function in regulation of many cellular processes including cell proliferation. Investigation the specific roles of eIF-5A involved in T. gondii is instrumental for the elucidation of tachyzoite replication. Here, eIF-5A knockdown strain was generated and analyzed by isobaric tags for relative and absolute quantification (iTraq), which suggested that proto-oncogene eIF-5A also acts as an essential gene to ensure proper protein synthesis during T. gondii invasion and replication.

2021-09-09 | PXD016810 | Pride

Mus musculus

Project description:Differences in gene expression patterns in mouse embryonic fibroblast Flp-In-3T3 cell lines stably expressing Pax6 or Pax6(5a).

| PRJNA145725 | ENA

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