Identification of PAX6 target genes in enteric precursor cells
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA631741 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR11771900.fastq.gz | Fastqsanger.gz | |||
| SRR11771901.fastq.gz | Fastqsanger.gz | |||
| SRR11771902.fastq.gz | Fastqsanger.gz | |||
| SRR11771903.fastq.gz | Fastqsanger.gz | |||
| SRR11771904.fastq.gz | Fastqsanger.gz |
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Project description:With the aim to elucidate the mechanism underlying the PAX6 role in such processes, we have performed a chromatin immunoprecipitation coupled with massively parallel sequencing (ChIP-Seq) analysis to identify the PAX6 target genes in enteric precursor cells (EPCs) from mice.
2020-11-26 | GSE150295 | GEO
Project description:With the aim to elucidate the mechanism underlying the DNMT3b role in such processes, we have performed a chromatin immunoprecipitation coupled with massively parallel sequencing (ChIP-Seq) analysis to identify the DNMT3B target genes in enteric precursor cells (EPCs) from mice.
2017-09-06 | GSE92942 | GEO
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.
2015-07-09 | GSE66961 | GEO
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
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.
2012-03-22 | GSE31402 | GEO
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
Project description:This is an integrative genome-wide approach to identify downstream networks controlled by Pax6 during mouse lens and forebrain development. Differential gene expression was analyzed in Pax6 mouse heterozygous and wildtype newborn mouse lenses, with subsequent comparison of this data with Pax6 forebrain expression data (Holm et al., 2007). Keywords: Differential gene expression
2008-10-17 | GSE13244 | GEO
Project description:PURPOSE. Limbal stem/progenitor cells (LSC) continuously proliferate and differentiate to replenish the corneal epithelium and play a vital role in corneal function and normal vision. Previous study revealed that Paired box 6 (PAX6) is a master transcription factor involved in determining the fate of corneal epithelial cells (CEC). However, the molecular events downstream of PAX6 remain largely unknown. In this study, we aimed to clarify the regulation network of PAX6 in driving CEC differentiation. METHODS. An air-liquid culture system was used to differentiate LSC into mature CEC. Specific targeting PAX6 short-hairpin shRNAs were used to knock down PAX6 in LSC. RNA-seq was used to analyze shPAX6-transfected CEC and CEC differentiation-associated genes to identify the potential downstream targets of PAX6. RNA-seq analysis, quantitative real-time PCR, and immunofluorescence staining were performed to clarify the function of WNK lysine deficient protein kinase 2 (WNK2), a downstream target of PAX6, and its relationship with corneal diseases. RESULTS. WNK2 expression increased during CEC differentiation and decreased upon PAX6 depletion. The distribution of WNK2 was specifically limited to the central corneal epithelium and suprabasal layer of the limbus. Knockdown of WNK2 impaired the expression of CEC-specific markers (KRT12, ALDH3A1, and CLU), disrupted the corneal differentiation process, and activated the terms of keratinization, inflammation, and cell proliferation, consistent with PAX6-depleted CEC and published microbial keratitis. Thus, aberrant expression of WNK2 was linked to corneal ulcers. CONCLUSIONS. As a downstream target of PAX6, WNK2 plays an essential role in corneal epithelial cell differentiation and maintenance of corneal homeostasis.
2024-10-30 | GSE272034 | GEO
Project description:Searching of target genes of miR-193b by transcriptome assay using 44K Whole Human Genome Microarray system (Agilent Technologies, Palo Alto, CA) resulted in finding of several candidate genes. To search of targets genes of miR-193b, we performed transcriptome analysis to compare expression profiles between human pancreatic cancer cells, MIA PaCa-2, transfected with precursor of miR-193b and those transfected with a negative control precursor.
2012-03-14 | E-GEOD-25215 | biostudies-arrayexpress
Project description:Pax6 is a transcription factor that is expressed in neuroepithelial cells from the initial stage of brain development. Region specific expression of Pax6 plays pivotal roles in the developing CNS, including brain patterning, neuronal specification, neuronal migration, and axonal projection. Regarding neurogenesis, Pax6 multiply works either as to promote neuronal differentiation or cell proliferation in a highly context-dependent manner. However, no Pax6 target gene is identified as to promote proliferation and/or inhibit differentiation of neuroepithelial cells. Here, we performed comparative analysis using the Affymetrix U34A array to identify genes that are differentially expressed in the early stage of wild-type and Pax6 homozygous mutant rat (rSey2/rSey2) brains. Keywords = Pax6 transcription factor Keywords = rat Keywords = forebrain and hindbrain regions of the wild-type or Pax6 homozygous embryos Keywords = up-or down-regulated genes Keywords: ordered
2005-10-06 | GSE2272 | GEO