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RNA-Seq transcriptome analysis of whole newborn lenses from FVB/N, Le-Cre and P0-3.9GFPCre mice

ABSTRACT: RNA-Seq transcriptome analysis of whole newborn lenses from FVB/N, Le-Cre and P0-3.9GFPCre mice

PROVIDER: PRJNA515262 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8443730.fastq.gz	Fastqsanger.gz
	SRR8443722.fastq.gz	Fastqsanger.gz
	SRR8443723.fastq.gz	Fastqsanger.gz
	SRR8443724.fastq.gz	Fastqsanger.gz
	SRR8443725.fastq.gz	Fastqsanger.gz

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RNA-Seq transcriptome analysis of whole newborn lenses from FVB/N, Le-Cre and P0-3.9GFPCre mice

Project description:Here we report RNA-Seq data from RNA isolated from newborn lenses from FVB/N control mice as well as from newborn lenses of two different transgenic mouse lines (Le-Cre and P0-3.9GFPCre). Sequence reads of 51 bp were obtained from an illumine HiSeq 2000 system and mapped to the C57BL/6 reference genome (assembly GRCm38 (mm10)) using GSNAP software. Adapters and poor-quality regions were trimmed using Trimmomatic-0.36 software. Gene and isoform abundance was quantified using RSEM-1.3.0 software. Differential expression analysis was completed using DESeq2-1.10.1 software. For differential expression we used a cutoff value of equal to or greater than 1.5-fold change with an adjusted p value ≤ 0.05. The transcriptomes of both Le-Cre and P0-3.9GFPCre lenses closely matched the FVB/N control lenses. However, Le-Cre lenses exhibited deregulation of 15 murine genes, several of which are associated with apoptosis. In contrast, P0-3.9GFPCre lenses only deregulated two murine genes.

2019-02-26 | GSE125108 | GEO

Transcription profiling of mouse LE-AP-2a mutants vs. wild-type P0 littermate lenses to investigate cell autonomous roles for AP-2alpha in lens vesicle separation and maintenance of the lens epithelial cell phenotype.

Project description:This is a comparative microarray analysis of LE-AP-2a mutants vs. wild-type P0 littermate lenses. This analysis revealed differential gene expression of 415 mRNAs, including reduced expression of genes important for maintaining lens epithelial cell phenotype, such as E-cadherin. Experiment Overall Design: Biological triplicates of mouse lenses were analyzed (three wild-type lens samples and three Le-AP-2 mutant samples)

2009-01-31 | E-GEOD-14536 | biostudies-arrayexpress

Transcription profiling of mouse Pax6 heterozygous and wildtype newborn mouse lenses

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). Experiment Overall Design: Three biological replicate experiments were performed from wildtype and heterozygote mice.

2008-10-26 | E-GEOD-13244 | biostudies-arrayexpress

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Lenses expression profile of DBL oncogene transgenic mice

Project description:The Dbl family of proteins represents a large group of proto-oncogenes involved in cell growth regulation. Alterations of the normal function of these proteins lead to pathological processes such as developmental disorders and neoplastic transformation. We have generated transgenic mice introducing the onco-Dbl cDNA sequences linked to the metallothionein promoter into the germ line of FVB mice and found that onco-Dbl expression affected proliferation, migration and differentiation of lens epithelial cells. We used high density oligonucleotide microarray to define the transcriptional profile induced by Dbl in the lenses of transgenic mice and observed modulation of genes encoding proteins promoting epithelial-mesenchymal transition (EMT). Moreover, genes encoding proteins involved in the positive regulation of apoptosis were markedly down regulated while anti-apoptotic genes were strongly up-regulated. Finally, several genes encoding proteins involved in the process of angiogenesis were up-regulated. These observations were validated by histological and immunohistochemical examination of the transgenic lenses, where vascularization can be readily observed. Thus, onco-Dbl expression in mouse lenses induces disruption of the lens architecture, epithelial cell proliferation, EMT, evasion from cell death, and aberrant angiogenesis. Whole lenses were removed from 2, 14, and 42 day old Dbl transgenic and wild type mice. 4 to 8 individual lenses were pooled . Three independent pools from each time and condition were used as replicates.

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Lenses expression profile of DBL oncogene transgenic mice

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Mus musculus musculus strain:FVB/N

Project description:Transcriptome analysis of epithelial and fiber cells from newborn mouse lenses

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HSF4 microarray gene expression analysis in the newborn mouse lens.

Project description:Differential expression of HSF4 in null newborn mouse and wildtype lenses was examined to identify putative downstream targets of HSF4. To examine roles of Brg1 in mouse lens development, a dnBrg1 transgenic construct was expressed using the lens-specific aA-crystallin promoter in postmitotic lens fiber cells. Morphological studies revealed abnormal lens fiber cell differentiation in transgenic lenses resulting in cataract. Electron microscopic studies showed abnormal lens suture formation and incomplete karyolysis (denucleation) of lens fiber cells. To identify genes regulated by Brg1, RNA expression profiling was performed in E15.5 embryonic wild type and dnBrg1 transgenic lenses. In addition, comparisons between differentially expressed genes in dnBrg1 transgenic, Pax6 heterozygous, and Hsf4 homozygous lenses identified multiple genes co-regulated by Brg1, Hsf4 and Pax6. Among them DNase IIb, a key enzyme required for lens fiber cell denucleation, was found downregulated in each of the Pax6, Brg1 and Hsf4 model systems. Lens-specific deletion of Brg1 using conditional gene targeting demonstrated that Brg1 was required for lens fiber cell differentiation and indirectly for retinal development but was not essential for lens lineage formation. Keywords: Differential mRNA Expression Three biological replicate experiments were performed with HSF null and wildtype lenses.

2010-12-01 | E-GEOD-22362 | biostudies-arrayexpress

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2008-02-03 | GSE7755 | GEO

Effect of pattern recognition receptor LE (PGRP-LE) overexpression in Dredd mutant Drosophila enterocytes

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