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Mucociliary epidermis RNA-seq data from comparison of controls and DN-tp63 morpholino knockdown in Xenopus animal cap explants.

ABSTRACT: This study was conducted to investigate the effects of DN-tp63 loss-of-function on mucociliary basal stem cells in Xenopus laevis. Uninjected control embryos and DN-tp63 morpholino oligonucleotide injected embryos were used to generate animal cap explants at embryonic stage 8. Explants were grown into mucociliary organoids and collected at embryonic stages 10.5, 16-19, and 24-25 for total RNA extraction.

ORGANISM(S): Xenopus laevis

PROVIDER: GSE130448 | GEO | 2019/04/30

REPOSITORIES: GEO

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Mucociliary epidermis RNA-seq data from comparison of controls and DN-tp63 morpholino knockdown in Xenopus animal cap explants.

Project description:Mucociliary epidermis RNA-seq data from comparison of controls and DN-tp63 morpholino knockdown in Xenopus animal cap explants.

| PRJNA540273 | ENA

Mucociliary epidermis RNA-seq data from controls and after manipulation of cell fates by Notch (suh-dbm, nicd) and cell type controlers (Foxa1MO, dnMCIDAS)

Project description:This study was conducted to investigate the effects of enriching or depleting cell types in mucociliary organoids in Xenopus laevis. (1) Uninjected control embryos were compared to (2) inhibition of Notch signaling (suh-dbm) which enriches ionocytes and multiciliated cells, (3) inhibition of Notch and suppression of MCIDAS (suh-dbm + dnMCIDAS) which enriches ionocytes and depletes multiciliated cells, (4) overactivation of Notch (nicd) which suppresses ionocytes and multiciliated cells and promotes small secretory cells and basal cells, (5) knockdown of foxa1 (foxa1MO) which depletes small secretory cells. Embryos were injected at 2-4 cell stage and were used to generate animal cap explants at embryonic stage 8. Explants were grown into mucociliary organoids and collected at embryonic stages 10.5, 16, 25, and 32 for total RNA extraction.

2022-10-18 | GSE215373 | GEO

microRNAs signatures of Xenopus laevis embryo epidermis at stage 11 (non ciliated) and 26 (ciliated) using high throughput sequencing

Project description:Epidermis of Xenopus embryos forms a mucociliary epithelium constituted of basal, scattered, secreting and ciliated cells and is histologically similar to human airway mucociliary epithelium. We compared microRNAs signatures of epidermis of Xenopus embryos at stage 11.5 (gastrula, non ciliated epidermis) and at stage 26 (tailbud, ciliated epidermis). 2 technical replicates of a pool of 50 explants for each stage 11.5 (non ciliated) and 26 (ciliated) of Xenopus laevis development

2011-06-06 | E-GEOD-22146 | biostudies-arrayexpress

Transciptome analysis of TP63 regulated pathways in HNSCC

Project description:Purpose: To identify TP63 expression regulated pathways in HNSCC Methods: A recombinant lentivirus encoding either NS shRNA or TP63 shRNA was introduced into a HNSCC cell line, FaDu. SCCs were gene generated by implanting either FaDu-NS shRNA (n=3) or FaDu-TP63 shRNA into the tongue of athymic nude mice. Tongue SCCs harvested at the end of study were used for transcriptome analysis

2019-03-15 | GSE120689 | GEO

The role of TP63 fusion in mouse lymphomagenesis

Project description:Patients with lymphoma harboring TP63 rearrangements have aggressive clinical course and dismal prognosis with no target therapy available. Thus, there is an urgent need to elucidate the molecular mechanisms and to develop novel therapeutic options for these patients. We then generated a TBL1XR1::TP63 fusion knockin trangenic mouse model and crossed with CD2/iCre mouse. This project is to study the role and function of TP63 fusion in mouse lymphomagenesis.

2023-10-01 | GSE240201 | GEO

Genome wide characterization reveals complex interplay between TP53 and TP63 in response to genotoxic stress [ChIP-Seq]

Project description:In response to genotoxic stress the TP53 tumour suppressor activates target gene expression to induce cell cycle arrest or apoptosis depending on the extent of DNA damage. These canonical activities can be repressed by TP63 in normal stratifying epithelia to maintain proliferative capacity or drive proliferation of squamous cell carcinomas, where TP63 is frequently overexpressed/amplified. Here we use ChIP-sequencing, integrated with microarray analysis, to define the genome wide interplay between TP53 and TP63 in response to genotoxic stress in normal cells. We reveal that TP53 and TP63 bind to overlapping, but distinct cistromes of sites through utilization of distinctive consensus motifs and that TP53 is constitutively bound to a number of sites. We demonstrate that cisplatin and adriamycin elicit distinct effects on TP53 and TP63 binding events, through which TP53 can induce or repress transcription of an extensive network of genes by direct binding and/or modulation of TP63 activity. Collectively, this results in a global TP53 dependent repression of cell cycle progression, mitosis and DNA damage repair concomitant with activation of anti-proliferative and pro-apoptotic canonical target genes. Further analyses reveals that in the absence of genotoxic stress TP63 plays an important role in maintaining expression of DNA repair genes, loss of which results in defective repair Examination of p63 and p53 binding sites in neonatal foreskin keratinocytes in response to adriamycin or cisplatin treatment

2014-04-11 | E-GEOD-56674 | biostudies-arrayexpress

Functional studies of TP63-affected ESCC tumor immune microenvironment

Project description:Our preliminary data from unbiased analyses of both ESCC patient samples and cell lines identified interferon-γ (IFN-γ) signaling pathway as the most significantly enriched pathways suppressed by TP63. To validate the activation of IFN pathways and the immune responses upon silencing of TP63, we utilized immune-competent mice to conduct allograft experiments. To analyze the effect of TP63 on ESCC tumor microenvironment, resected tumors were then collected to perform scRNA-seq.

2024-02-29 | GSE221938 | GEO

Genome wide characterization reveals complex interplay between TP53 and TP63 in response to genotoxic stress [Affymetrix]

Project description:In response to genotoxic stress the TP53 tumour suppressor activates target gene expression to induce cell cycle arrest or apoptosis depending on the extent of DNA damage. These canonical activities can be repressed by TP63 in normal stratifying epithelia to maintain proliferative capacity or drive proliferation of squamous cell carcinomas, where TP63 is frequently overexpressed/amplified. Here we use ChIP-sequencing, integrated with microarray analysis, to define the genome wide interplay between TP53 and TP63 in response to genotoxic stress in normal cells. We reveal that TP53 and TP63 bind to overlapping, but distinct cistromes of sites through utilization of distinctive consensus motifs and that TP53 is constitutively bound to a number of sites. We demonstrate that cisplatin and adriamycin elicit distinct effects on TP53 and TP63 binding events, through which TP53 can induce or repress transcription of an extensive network of genes by direct binding and/or modulation of TP63 activity. Collectively, this results in a global TP53 dependent repression of cell cycle progression, mitosis and DNA damage repair concomitant with activation of anti-proliferative and pro-apoptotic canonical target genes. Further analyses reveals that in the absence of genotoxic stress TP63 plays an important role in maintaining expression of DNA repair genes, loss of which results in defective repair Examination of gene expression levels of HFKS siRNA depleted for p53 or p63 in response to adriamycin or cisplatin treatment We analyzed RNA using the Affymetrix Human Exon 1.0 ST platform. Array data was processed using the AltAnalyze.

2014-04-30 | E-GEOD-57187 | biostudies-arrayexpress

Down-regulation of MYC and TP63 in human keratinocytes

Project description:This transcriptome study is intended to discover the effects of MYC and TP63 on human keratinocytes differentiation at the genome level. Human keratinocyte cell line, HaCaT cells were transfected by siRNAs with the help of transfection reagent, INTERFERin. 48 hours post-transfection, total RNA was extracted from cells. We used a non-targeting siRNA as a negative control. siRNA targeting MYC or TP63 was obtained from QIAGEN, and RNAs from wild type HaCaT cells were used as reference samples. We did 3 biological replicates and 2 'dye swap' for each sample. Totally we got 12 samples, with 2 dye-swap for each sample, and 48 arrays used for all hybridization.

2010-05-15 | E-GEOD-17394 | biostudies-arrayexpress

ChIP-seq for TP63 transcription factor in primary CLL cells

Project description:Identification of TP63 binding profile (cistrome) at a genome-wide scale, in primary cells derived from patient diagnosed with Chronic Lymphocytic Leukemia.

2022-03-07 | E-MTAB-10717 | biostudies-arrayexpress

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