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RNA-seq analysis of hES-RPE cells in 14d from LHX2 KD and control - non-specific shRNA

ABSTRACT: RNA-seq analysis of hES-RPE cells in 14d from LHX2 KD and control - non-specific shRNA

PROVIDER: PRJNA737495 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR14808634.fastq.gz	Fastqsanger.gz
	SRR14808635.fastq.gz	Fastqsanger.gz
	SRR14808636.fastq.gz	Fastqsanger.gz
	SRR14808637.fastq.gz	Fastqsanger.gz

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RNA-seq analysis of hES-RPE cells in 14d from LHX2 KD and control - non-specific shRNA

Project description:RNA-seq analysis was applied in duplicates to hES-RPE cells in 14d: LHX2-KD and control - non-specific shRNA

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ChIP-seq analysis of LHX2 in hES-RPE cells

Project description:LHX2 binding sites were profiled in RPE cells generated from human embryonic stem cells (hES-RPE)

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ChIP-seq analysis of LHX2 in hES-RPE cells

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ChIP-seq analysis of SOX9 in hES-RPE cells

Project description:SOX9 binding sites were profiled in RPE cells generated from human embryonic stem cells (hES-RPE)

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ChIP-seq analysis of OTX2 in hES-RPE cells

Project description:OTX2 binding sites were profiled in RPE cells generated from human embryonic stem cells (hES-RPE)

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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

ChIP-seq analysis of SOX9 in hES-RPE cells

Project description:ChIP-seq analysis of SOX9 in hES-RPE cells

| PRJNA470901 | ENA

ChIP-seq analysis of OTX2 in hES-RPE cells

Project description:ChIP-seq analysis of OTX2 in hES-RPE cells

| PRJNA737497 | ENA

Characterization of hES derived Retinal Pigment Epithelial (RPE). RPE proliferation involves a non-classical Epithelial-Mesenchymal Transition (EMT).

Project description:Retinal Pigment Epithelial (RPE) cells are located behind the retina and are critical for photoreceptor survival. Loss of RPE is associated with several pathogenic conditions such as Age Related Macular Degeneration and Retinitis Pigmentosa. RPE derived from human embryonic stem cells (hESC) offer a potential source for producing these cells for therapy. Here we report the molecular and cellular characterization of RPE differentiated from hESC. hESC derived RPE are capable of proliferation and lose their epithelial characteristics before becoming confluent and re-differentiating back into their typical pigmented, cobblestoned appearance. During the proliferative phase, they adopt a mesenchymal morphology and express mesenchymal markers. Our results demonstrate that this apparent Epithelial-Mesenchymal Transition is not regulated by the classical EMT transcription factors SNAIL and SLUG. Furthermore, it is possible to regulate RPE de-differentiation and re-differentiation by modulating the Wnt and BMP pathway respectively. These findings further our understanding of the genesis and expansion of RPE which is essential for their therapeutic use.

2012-10-24 | E-MTAB-854 | biostudies-arrayexpress

Transcription profiling of mouse cells expressing tet inducible LhX2, withdrawal of LHX2 over time was analysed

Project description:Expression of the lim-homeodomain transcription factor is required for sustained maintenance of heamatopoietic stem cell like cells in undifferentiated form durng in vitro culturing. Cell lines were created from the mouse embryonic stem (ES) cell line, Ainv15. The gene Lhx2 was introducted into these cells under the control of a tetracycline-responsive element. In the presence of tetracycline (or its analogue doxycycline), these cells express Lhx2. In DoxHPC7 GFP is co-expressed together with the Lhx2 gene. We used these cells to carry out a time-course study where the effects of Lhx2 withdrawal were studied.

2005-12-19 | E-MEXP-431 | biostudies-arrayexpress

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