GEO DataSets

(Submitter supplied) OTX2 binding sites were profiled in RPE cells generated from human embryonic stem cells (hES-RPE)

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18573

4 Samples

Download data: BED

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18573

13 Samples

Download data

(Submitter supplied) LHX2 binding sites were profiled in RPE cells generated from human embryonic stem cells (hES-RPE)

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18573

5 Samples

Download data: BED

(Submitter supplied) RNA-seq analysis was applied in duplicates to hES-RPE cells in 14d: LHX2-KD and control - non-specific shRNA

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

4 Samples

Download data: XLSX

(Submitter supplied) 11 samples total with libraries prepared on 10X Chromium. Corresponding to 4 control eyes.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

11 Samples

Download data: TXT

(Submitter supplied) Bulk RNAseq of retina and RPE/choroid tissue, each from the macula or non-macula (peripheral) regions of human donor eyes.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

537 Samples

Download data: TSV

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus

Type:

Expression profiling by array; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL13112 GPL6887

22 Samples

Download data

(Submitter supplied) ChIP-seq using anti-Lhx1 antibody to map genomic binding of Lhx1 in stably transfected P19 mouse embryonic carcinoma cells

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13112

6 Samples

Download data: WIG

(Submitter supplied) Expression profiling of wild-type and Lhx1 null mouse definitive endoderm cultures using Illumina whole genome mouse V2 arrays. The hypothesis tested was that Lhx1 regulates gene expression of definitive endoderm and anterior mesendoderm genes

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6887

16 Samples

Download data: TXT

(Submitter supplied) Age-related macular degeneration (AMD) is a leading cause of blindness in the elderly. The extent to which epigenetic changes regulate the progression of AMD is unclear. Here we profiled chromatin accessibility in the retina and retinal pigmented epithelium (RPE) from AMD patients and controls. Global decreases in chromatin accessibility occur in the RPE in early AMD and in the retina with advanced disease. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:

GPL15520 GPL16791

58 Samples

Download data: NARROWPEAK, TXT

(Submitter supplied) Otx2 has been shown to be non cell autonomously required for photoreceptor cell survival in the adult mouse RPE. This study aims to identify Otx2 DNA binding profile in both RPE and neural retina to i) identify direct targets of Otx2 in the RPE ii) compare Otx2 binding profile in neural retina and RPE to unveil hidden functions in the neural retina.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11002

7 Samples

Download data: BED

(Submitter supplied) During embryonic development, tissue-specific transcription factors and chromatin remodelers function together to assure the gradual, coordinated differentiation of multiple lineages. Here, we study this regulatory interplay in the developing retinal pigmented epithelium (RPE), a neuroectodermal lineage essential for the development, function, and maintenance of the adjacent retina. We present a high-resolution spatial transcriptomic atlas of the developing mouse RPE and the adjacent ocular mesenchyme, obtained by geographic positional sequencing (Geo-Seq) of a single development stage of the eye, encompassing young and more mature ocular progenitors. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

112 Samples

Download data: TXT

(Submitter supplied) We evaluate whether human induced pluripotent stem cell-derived retinal pigment epithelium (iPSC-RPE) cells can be used to prioritize and functionally characterize causal variants at age-related macular degeneration (AMD) risk loci. We generated iPSC-RPE from six subjects and show that they have morphological and molecular characteristics similar to native RPE. We generated RNA-seq, ATAC-seq, and H3K27ac ChIP-seq data and observe high similarity in gene expression and enriched transcription factor motif profiles between iPSC-RPE and human fetal-RPE. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20301

24 Samples

Download data: BW, TSV

(Submitter supplied) We previously demonstrated that hematopoietic stem cell (HSC)-like cells are robustly expanded from mouse embryonic stem (ES) cells by enforced expression of Lhx2, a LIM-homeobox domain (LIM-HD) transcription factor. Here we established an ES cell line which conditionally expressed Lhx2 by Tet-On system. The ES cells were differentiated into HSC-like cells by Lhx2 expression. Lhx2-regulated genes were identified by comparing the HSC-like cells with those cultured in the absence of Lhx2 expression.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL5642

1 Sample

Download data: GPR

(Submitter supplied) Utilize high-throughput transcriptomic and cistromic analysis to determine the functional requirement for LDB1 and ISL1 in mature murine pancreatic β-cells while simultaneously assessing their functional interdependence at the chromatin level.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17021

21 Samples

Download data: BED, BW, XLSX

(Submitter supplied) To determine mouse retinal pigment epithelium (RPE) specific gene expression, we compared the gene expression profile of the RPE to the gene expression of its adjacent layers: the choroid (CH) and photoreceptors (PR). We collected the tissues using the meticulous laser dissection microscopy. Next, we performed RNA isolation, amplification, labeling and hybridization against 44k Agilent microarrays. Compared RPE gene expression with CH gene expression, and with PR gene expression

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL10333

9 Samples

Download data: TXT

(Submitter supplied) Comparing iPS derived RPE cells from human AMD and non-AMD donors It has been a challenge to model retinal disorders such as geographic atrophy (GA) in in vivo animals, primarily because several factors, including genetics and aging itself, contribute to disease phenotype of age-related macular degeneration (AMD). We generated retinal pigment epithelial (RPE) cells from patients with advanced AMD and assessed their ability to model disease. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL23159

7 Samples

Download data: CEL, TXT

(Submitter supplied) 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.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL10787

6 Samples

Download data: TXT

(Submitter supplied) SOX9 binding sites were profiled in RPE cells generated from human embryonic stem cells (hES-RPE)

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL16791

8 Samples

Download data: BED

(Submitter supplied) Homeobox transcription factor Otx2 is a key actor in retinal development, but in adult stage its function is not yet elucidated. In order to elucidate it we induced Otx2 KO specifically in MATURE PHOTORECEPTORS. Here, we report RNA seq data, that were produced in order to investigate on the effect of Otx2 ablation on its regulatoy network. Post natal day 30 (P30) is the time of KO induction. KO mice were collected 2, 4 and 8 days after Otx2 ablation. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

12 Samples

Download data: TXT