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Next generation sequencing of chicken otocyst with pharmacologically induced loss-of-Wnt signalling

ABSTRACT: Next generation sequencing of chicken otocyst with pharmacologically induced loss-of-Wnt signalling

PROVIDER: PRJNA627935 | ENA |

REPOSITORIES: ENA

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Dataset's files

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			Action	DRS
	SRR11606850_1.fastq.gz	Fastqsanger.gz
	SRR11606850_2.fastq.gz	Fastqsanger.gz
	SRR11606851_1.fastq.gz	Fastqsanger.gz
	SRR11606851_2.fastq.gz	Fastqsanger.gz
	SRR11606852_1.fastq.gz	Fastqsanger.gz

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Next generation sequencing of chicken otocyst with pharmacologically induced loss-of-Wnt signalling

Project description:Bulk RNA-sequencing of individual E2.5 chicken otocyst incubated in media enriched with Wnt signalling inhibitor IWR-1 or control condition (DMSO) for 24h. Transcripts abundance was mapped to a chicken reference genome using Kallisto package and differentially expressed genes were identify using Sleuth package (genes with p-value < 0.05 were considered as significant). The expression of 1340 genes was significantly changed:733 genes were up-regulated and 607 were down-regulated. Biological Function enrichment analysis (Toppgene online tool) showed that many of these genes were associated with neurogenesis.

2020-12-01 | GSE149310 | GEO

Next generation sequencing of chicken otocyst with pharmacologicaly induced loss-of-Wnt signalling

Project description:Bulk RNA-sequencing of individual E2.5 chicken otocyst incubated in media enriched with Wnt signalling inhibitor IWR-1 or control condition (DMSO) for 24h. Transcripts abundance was mapped to a chicken reference genome using Kallisto package and differentially expressed genes were identify using Sleuth package (genes with p-value < 0.05 were considered as significant). Biological Function enrichment analysis (Toppgene online tool) showed that many of these genes were associated with neurogenesis.

2021-04-01 | GSE161638 | GEO

Next generation sequencing of chicken otocyst with genetically induced loss-of-Wnt signalling

Project description:Bulk RNA-sequencing of individual E3 chicken otocyst, in which Wnt signaling activity was reduced by genetic manipulation. The E2 otic placodes were in ovo transfected with a construct overexpressing truncated form of B-catenin reducing Wnt activity or a control plasmid expressing mCherry and collected 24h later. Transcripts abundance was mapped to a chicken reference genome using Kallisto package and differentially expressed genes were identify using Sleuth package (genes with p-value < 0.05 were considered as significant).

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Next generation sequencing of chicken otocyst with pharmacologicaly induced loss-of-Wnt signalling

Project description:Next generation sequencing of chicken otocyst with pharmacologicaly induced loss-of-Wnt signalling

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Next generation sequencing of chicken otocyst with genetically induced loss-of-Wnt signalling

Project description:Next generation sequencing of chicken otocyst with genetically induced loss-of-Wnt signalling

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Next generation sequencing of chicken otocyst with gain- and loss-of-Notch signalling activity

Project description:Bulk RNA-sequencing of individual chicken otocysts, in which Notch activity was either stimulated or blocked. To stimulate Notch activity, the E2 otic placodes were in ovo transfected with a construct overexpressing Notch1 Intracellular domain (NICD1) or a control plasmid expressing mRFP1 and collected 6h or 24h later. To pharmacologically block Notch activity, E2.5 chicken otocysts were incubated in media enriched with γ-secretase Inhibitor or control condition (DMSO) for 6h or 24h. Transcripts abundance was mapped to a chicken reference genome using Kallisto package.

2022-12-01 | GSE196999 | GEO

Analysis of Gene Expression in the Chicken Otocyst

Project description:The inner ear arises from multipotent placodal precursors that are gradually committed to the otic fate and further differentiate into all inner ear cell types, with the exception of a few neural crest-derived cells. The otocyst has a pivotal role during inner ear development: otic progenitor cells sub-compartmentalize into non-sensory regions and regions giving rise to prosensory domains where subsequently also hair cells differentiate. The genes and pathways underlying this progressive subdivision and differentiation process are not entirely known. The goal of this study was to identify a comprehensive set of genes expressed in the chicken otocyst using the serial analysis of gene expression (SAGE) method. Our analysis revealed several hundred transcriptional regulators, potential signaling proteins, and receptors. We identified a substantial collection of genes that were previously known in the context of inner ear development, but we also found many new candidate genes, such as Sox4, Sox5, Sox7, Sox8, Sox11, and Sox18, which previously were not known to be expressed in the developing inner ear. Despite its obvious limitation of not being all-inclusive, the generated otocyst SAGE library is a practical bioinformatics tool to study otocyst gene expression and to identify candidate genes for developmental studies. Otocysts were dissected from HH stage 18-19 chicken embryos, total RNA was extracted, and subjected to a commercial long-SAGE protocol, resulting in a library of concatemerized tags. 3,512 individual clones of SAGE concatemers were sequenced resulting in 39,326 17-bp tags with tag counts up to 718 for the most abundant tag; 3,292 tags that were represented between two and five times, whereas the majority of tags (11,717) were only found once. Overall, we identified 16,008 unique sequence tags.

2011-03-01 | E-GEOD-27176 | biostudies-arrayexpress

Analysis of Gene Expression in the Chicken Otocyst

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Next generation sequencing of chicken otocyst with gain- and loss-of-Notch signalling activity

Project description:Next generation sequencing of chicken otocyst with gain- and loss-of-Notch signalling activity

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Project description:Hypothesis and proof of concept: Our hypothesis is that increase in cellular iron import proteins (TfR1, DMT1) occur early in the adenoma-carcinoma sequence through mutations in APC and lead to cellular iron loading. As demonstrated in our previous work the effects of this iron loading is to mediate increased Wnt signalling resulting in c-myc induction. This in turn serves to increase the expression of iron import proteins (TfR1, DMT1) and decrease the expression of iron export (ferroportin [FPN]) and storage (ferritin) proteins. Such a hypothesis explains how Wnt signalling controls iron metabolism and ensures that there is adequate cellular iron for ATP generation and cellular proliferation. Experimental design: To test such a hypothesis we aim to prospectively collect the following colorectal tissue from patients attending for colonoscopy: 1. Normal colonic mucosa in patients with no colorectal pathology (n = 30) 2. Polyps and matched normal colon (n = 30) 3. Colorectal cancers and matched normal colon (n = 30) We also intend to collect serum and urine from the following patient groups: 4. Normal colonoscopy (n = 30) 5. Colorectal adenomas (n = 30) 6. Colorectal cancers (n = 30) Primary outcome(s): Measured at baseline, using the expression of proteins in the tissue and serum to detect the cellular and systemic iron transport proteins. The techniques used will include mass spectrometry, western blotting, real time PCR and immunohistochemistry.

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