Ontology highlight
ABSTRACT:
PROVIDER: PRJNA534430 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8949030_1.fastq.gz | Fastqsanger.gz | |||
| SRR8949030_2.fastq.gz | Fastqsanger.gz | |||
| SRR8949031_1.fastq.gz | Fastqsanger.gz | |||
| SRR8949031_2.fastq.gz | Fastqsanger.gz | |||
| SRR8949032_1.fastq.gz | Fastqsanger.gz |
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Project description:Healthy placental development is essential for reproductive success; failure of the feto-maternal interface results in preeclampsia and intrauterine growth retardation. We found that grainyhead-like 2 (GRHL2), a CP2-type transcription factor, is highly expressed in chorionic trophoblast cells, including basal chorionic trophoblast (BCT) cells located at the chorioallantoic interface in murine placentas. Placentas from Grhl2-deficient mouse embryos displayed defects in BCT cell polarity and basement membrane integrity at the chorioallantoic interface, as well as a severe disruption of labyrinth branchingmorphogenesis.Selective Grhl2 inactivation only in epiblastderived cells rescued all placental defects but phenocopied intraembryonic defects observed in global Grhl2 deficiency, implying the importance of Grhl2 activity in trophectoderm-derived cells. ChIPseq identified 5282 GRHL2 binding sites in placental tissue. By integrating these data with placental gene expression profiles, we identified direct and indirect Grhl2 targets and found a marked enrichment of GRHL2 binding adjacent to genes downregulated in Grhl2−/− placentas, which encoded known regulators of placental development and epithelial morphogenesis. These genes included that encoding the serine protease inhibitor Kunitz type 1 (Spint1), which regulates BCT cell integrity and labyrinth formation. In human placenta, we found that human orthologs of murine GRHL2 and its targets displayed co-regulation and were expressed in trophoblast cells in a similar domain as in mouse placenta. Our data indicate that a conserved Grhl2-coordinated gene network controls trophoblast branching morphogenesis, thereby facilitating development of the site of feto-maternal exchange. This might have implications for syndromes related to placental dysfunction. In vivo genome-wide examination of binding sites of the transcription factor GRHL2 by ChIP-seq using wild-type murine E17.5 placenta tissue. Two samples in total: one GRHL2 ChIP sample and one IgG ChIP sample using wild-type placentas tissue as antibody control.
2015-03-10 | E-GEOD-65962 | biostudies-arrayexpress
Project description:Aim: Identify molecular pathways controlling palate closure Methods: First pharygneal arch of wild-type and Grhl2-/- e10.5 moues embryos was subjected to RNAseq Results: Grhl2-/- PA1 displayed a shift from epithelial to mesenchymal gene expression Conclusions: Grhl2 maintains epithelial cellular identity during palate closure
2020-03-03 | GSE106130 | GEO
Project description:Healthy placental development is essential for reproductive success; failure of the feto-maternal interface results in preeclampsia and intrauterine growth retardation. We found that grainyhead-like 2 (GRHL2), a CP2-type transcription factor, is highly expressed in chorionic trophoblast cells, including basal chorionic trophoblast (BCT) cells located at the chorioallantoic interface in murine placentas. Placentas from Grhl2-deficient mouse embryos displayed defects in BCT cell polarity and basement membrane integrity at the chorioallantoic interface, as well as a severe disruption of labyrinth branchingmorphogenesis.Selective Grhl2 inactivation only in epiblastderived cells rescued all placental defects but phenocopied intraembryonic defects observed in global Grhl2 deficiency, implying the importance of Grhl2 activity in trophectoderm-derived cells. ChIPseq identified 5282 GRHL2 binding sites in placental tissue. By integrating these data with placental gene expression profiles, we identified direct and indirect Grhl2 targets and found a marked enrichment of GRHL2 binding adjacent to genes downregulated in Grhl2−/− placentas, which encoded known regulators of placental development and epithelial morphogenesis. These genes included that encoding the serine protease inhibitor Kunitz type 1 (Spint1), which regulates BCT cell integrity and labyrinth formation. In human placenta, we found that human orthologs of murine GRHL2 and its targets displayed co-regulation and were expressed in trophoblast cells in a similar domain as in mouse placenta. Our data indicate that a conserved Grhl2-coordinated gene network controls trophoblast branching morphogenesis, thereby facilitating development of the site of feto-maternal exchange. This might have implications for syndromes related to placental dysfunction.
2015-03-10 | GSE65962 | GEO
Project description:Transcriptome analysis of Oct4 null and wild type preimplantation mouse embryos by RNA-sequencing
2013-06-06 | GSE47089 | GEO
Project description:Estrogen receptor (ER) positive breast cancer is characterized by a late recurrence following initial treatment. The epithelial cell fate transcription factor Grainyhead-like protein 2 (GRHL2) is amplified in ER positive breast cancers and is indicative of poorer prognosis as compared to ER negative breast cancer. To understand how GRHL2 contributes to progression, GRHL2 was overexpressed in ER positive cells. To determine how GRHL2 overexpression affects GRHL2 binding to DNA, ChIP sequencing was conducted to evaluate binding intensity and location.
2024-08-25 | GSE272059 | GEO
Project description:We previously identified that MLL3, also known as lysine methyltransferase 2C, is frequently mutated in Upper Aerodigestive Squamous Cell Carcinoma (UASCC). TCGA dataset also demonstrated that around 10% of UASCC patients have a mutation of MLL3. However, the significance of MLL3 in the context of premalignant biology and neoplastic evolution has not been well understood. Therefore, we aim to explore the functional contribution of MLL3 to the biology of UASCC in this study. We identified that MLL3 forms a protein complex with GRHL2 in the regulation of UASCC epigenome. To investigate the regulation of the downstream signaling pathway by MLL3/GRHL2 protein complex, ChIP sequencing using either MLL3 or GRHL2 antibodies was performed in UASCC cell line. In addition, either MLL3 or GRHL2 was silenced by transfection of siRNA and performed RNA-Sequencing in UASCC cell line (KYSE510) to profile the transcriptome.
2024-07-20 | GSE238111 | GEO
Project description:Estrogen receptor (ER) positive breast cancer is characterized by a late recurrence following initial treatment. The epithelial cell fate transcription factor Grainyhead-like protein 2 (GRHL2) is amplified in ER positive breast cancers and is indicative of poorer prognosis as compared to ER negative breast cancer. To understand how GRHL2 contributes to progression, GRHL2 was overexpressed in ER positive cells. To examine gene expression changes from elevated GRHL2 levels, RNA-sequencing was performed to better comprehend how high GRHL2 may change its transcriptional activity.
2024-08-25 | GSE272061 | GEO
Project description:RNA sequencing was performed on RNA isolated from groups of 6 hpf wild type and mecp2-null embryos (n=3 biological replicates per condition with 30 embryos pooled per replicate). DESeq2 analysis was performed using https://usegalaxy.org/
2016-09-01 | GSE80348 | GEO
Project description:The airways of the human lung are lined by an epithelium made up of ciliated and secretory luminal cells and undifferentiated p63+ Krt5+ basal cells. The integrity of this epithelium and its ability to act as a selective barrier are critical for normal lung function. In other epithelia there is evidence that transcription factors of the evolutionarily conserved grainyheadlike (GRHL) family play key roles in co-ordinating the expression of numerous proteins required for epithelial morphogenesis, differentiation, remodeling and repair. However, little is known about their function in the adult lung. Here, we focus on the role of GRHL2 in primary human bronchial epithelial (HBE) cells, using either shRNA or a dominant negative protein (DN-GRHL2) to inhibit its function. We follow changes in epithelial phenotype, and in gene transcription using RNA-seq or microarray analysis, both in undifferentiated basal cells and in cells differentiating in air-liquid interface culture into a mucociliary epithelium with transepithelial electrical resistance. We identify several hundreds of genes that are directly or indirectly regulated by GRHL2. Using ChIP-seq to map sites of GRHL2 binding in the basal cells we identify 7,687 potential primary targets, and confirm that GRHL2 binding is strongly enriched near GRHL-regulated genes. Different subsets of the large cohort of potential GRHL2 targets appear to be active in basal and differentiated cells. Taken together, the results strongly support the hypothesis that GRHL2 plays a key role in regulating many physiological functions of human airway epithelium, including those involving cell adhesion, polarity and morphogenesis. Frozen primary human bronchial epithelial (HBE) cells were obtained from three donors and grown to confluence in standard culture conditions. Cells were crosslinked with formaldehyde and collected in aliquots of ~20M cells per donor. ChIP-seq for GRHL2 (Antibody: Sigma HPA004820) was then performed relative to an input control for each donor.
2013-05-07 | E-GEOD-46194 | biostudies-arrayexpress
Project description:RNA sequencing was performed on RNA isolated from groups of 6 hpf wild type and mecp2-null embryos (n=3 biological replicates per condition with 30 embryos pooled per replicate). DESeq2 analysis was performed using https://usegalaxy.org/ Whole embryo mRNA profile of 30 pooled mecp2-null or wild type 6 hpf zebrafish embryos, in triplicate, using the Illumina HiSeq4000 platform
2016-09-01 | E-GEOD-80348 | biostudies-arrayexpress