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RNA sequencing of E15.5 retinal tissue from control and Lhx2 CKO mice

ABSTRACT: RNA sequencing of E15.5 retinal tissue from control and Lhx2 CKO mice

PROVIDER: PRJNA723339 | ENA |

REPOSITORIES: ENA

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RNA sequencing of E15.5 retinal tissue from control and Lhx2 CKO mice

Project description:Lhx2 is a retinal progenitor cell transcription factor critical for eye development. We previously reported that conditional inactivation of Lhx2 at the start of mouse retinal neurogenesis disrupted retinal progenitor cell (RPC) proliferation, greatly reduced the RPC pool and altered neurogenic output as indicated by changes in the production of multiple fated precursor populations. To identify genes whose expression levels are dependent on Lhx2 at this stage of development, Lhx2 conditional inactivation was initiated at E11.5 in RPCs with the progenitor Cre driver Hes1CreERT2 and retinal tissue was collected at E15.5 for RNA sequencing. The gene expression profiles of Lhx2 CKO retinas were compared to control (Lhx2 conditional heterozygotes) were compared. Downregulated and upregulated gene expression was observed, with some likely due to direct and indirect regulation by Lhx2 within RPCs and others due to changes in differentiation and the altered neurogenic output.

2022-04-29 | GSE172457 | GEO

Expression profile of P7 control and Lhx2 cKO somatosensory cortex

Project description:Microarray analysis of control and Lhx2 cKO somatosensory cortices to determine differentially expressed genes at P7 resulting from the loss of Lhx2 in post-mitotic neurons.

2016-12-15 | GSE92372 | GEO

RNAseq analysis of the global retinal transcriptome of rod photoreceptor-specific Dicer1 conditional knockout mice and control littermates

Project description:We report RNAseq analysis of the transcriptome of retinas from mature rod-specific Dicer1 cKO mice and control littermates lacking Cre expression in order to better understand changes in gene regulation that could lead to retinal degeneration in cKO mice. Examine retinal transcriptome of 3 biological replicates for each genotype from 4-week-old animals with tissue collected between 8:00 - 10:00AM

2014-08-14 | E-GEOD-55377 | biostudies-arrayexpress

small RNAseq analysis of the global retinal transcriptome of rod photoreceptor-specific Dicer1 conditional knockout mice and control littermates

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RNA-seq analysis of RPE cells from Sox9 cKO and wild-type control mice

Project description:RNA-seq analysis was applied in triplicates to RPE cells extracted at two developmental time-points (E15.5 and P5) from Sox9-cKO and wild-type control mice

2018-07-17 | GSE114945 | GEO

TGFβ signaling in retinal tissue repair

Project description:TGFβ signaling in retinal tissue repair

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RNAseq analysis of the global retinal transcriptome of rod photoreceptor-specific Dicer1 conditional knockout mice and control littermates

2014-08-14 | GSE55377 | GEO

small RNAseq analysis of the global retinal transcriptome of rod photoreceptor-specific Dicer1 conditional knockout mice and control littermates

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The LHX2-OTX2 regulatory module controls RPE differentiation and underlies a causal regulatory risk-SNP in age-related macular degeneration

Project description:Tissue-specific transcription factors control the transcriptome through an association with noncoding regulatory regions (cistromes). Identifying the combination of transcription factors that dictate specific cell fate, their specific cistromes and examining their involvement in complex human traits remain a major challenge. Here we focus on the retinal pigmented epithelium (RPE), an essential lineage for retinal development and function and the primary tissue affected in age-related macular degeneration (AMD), a leading cause of blindness. By combining mechanistic findings in stem-cell-derived human RPE, in- vivo functional studies in mice and global transcriptomic and proteomic analyses, we revealed that the key developmental transcription factors LHX2 and OTX2 function together in transcriptional module containing LDB1 and SWI/SNF (BAF) to regulate the RPE transcriptome. Importantly, the intersection between the identified LHX2-OTX2 cistrome with published expression quantitative trait loci, ATAC-seq data from human RPE, and AMD GWAS data, followed by functional validation using a reporter assay, revealed a causal genetic variant that affects AMD risk by altering TRPM1 expression in the RPE through modulation of LHX2 transcriptional activity on its promoter. Taken together, the reported cistrome of LHX2 and OTX2, the identified downstream genes and interacting co-factors reveal the RPE transcription module and uncover a causal regulatory risk SNP in the multifactorial common blinding disease AMD.

2023-03-11 | PXD038485 | Pride

Lhx2 controls changes in chromatin accessibility in retinal progenitor cells during developmental competence transitions.

Project description:We profiled retinal progenitor cells by integrating next generation sequencing methods and interrogating changes in chromatin accessibility at embryonic and post-natal murine stages. We identified putative factors involved in the developmental progression of the retinal progenitors epigenome and we report Lhx2 role in the regulation of chromatin accessibility by coordinated action of developmentally regulated pioneer factors

2019-05-09 | GSE99818 | GEO

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