GEO DataSets

(Submitter supplied) Results: Our histologic studies indicated that human retinal organoids (HROs) at day 200 of differentiation in this system are postmitotic and thus completed retinogenesis. Further, HRO contain all major retinal cell types in a laminated structure. Notably, HROs are cone photoreceptor-rich, show a 1:1:1 ratio of Müller glia, rod and cone photoreceptor. Immunostaining and ultrastructural studies showed that photoreceptors neurons mature, including photoreceptor inner and nascent outer segment formation. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

1 Sample

Download data: H5AD, MTX, TSV

(Submitter supplied) The application potential of human induced pluripotent stem cells (hiPSC) derived human retinal organoids (HRO) relies on the robustness and transferability of the methodology for their generation. Standardized strategies and parameters to effectively assess, compare and optimize organoid protocols have been started to be established, but are not completed yet. To advance this, we explored the efficiency and reliability of a differentiation protocol that facilitates retina generation by formation of neuroepithelial cysts from hiPSC clusters. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

1 Sample

Download data: H5AD, MTX, TSV

(Submitter supplied) Methods: Profiles of individual human retinal organoids (HRO) at 150, 200 and 250 days of development days were treated for 10 days with HBEGF and TNF, and compared to solvent controls (CTRL). N=6 HROs per timepoint and variable. Single-end sequencing with 30 Mio reads per sample was performed at a length of 75 bases on HiSeq2500 (Illumina). The sequence reads that passed quality filters were analyzed at the transcripts level. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

36 Samples

Download data: TXT

(Submitter supplied) Photoreceptor loss is a leading cause of blindness, but mechanisms underlying photoreceptor degeneration are not well understood. Treatment strategies would benefit from an improved understanding of gene-expression patterns directing photoreceptor development, as many genes are implicated in both development and degeneration. Neural retina leucine zipper (NRL) is critical for rod photoreceptor genesis and degeneration, with NRL mutations known to cause enhanced S-cone syndrome and retinitis pigmentosa. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

17 Samples

Download data: TXT

(Submitter supplied) Methods: Mouse retinal organoids (MRO) profiles at day 20, 22, 25, and 30 in culture under control conditions. MROs were generated using the previously established trisection protocol (Völkner et al. 2016, 2019). Single-end sequencing with 30 Mio reads per sample was performed at a length of 75 bases on HiSeq2500 (Illumina). The sequence reads that passed quality filters were analyzed at the transcripts level. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

24 Samples

Download data: TXT

(Submitter supplied) To determine the best cell source for the development of hiPSCs, we established hiPSCs from three different hematopoietic stem cell sources, peripheral blood, cord blood and, bone marrow aspirates, and differentiated them into functional RBCs. We compared the characteristics of hiPSCs and hiPSC-derived erythroid cells using various time course studies. We then performed gene expression profiling analysis using samples obtained from RNA-seq at 4 time points for each source.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

15 Samples

Download data: XLSX

(Submitter supplied) Fresh retinatissues were harvested from 30 day old C57BL/6J mice according to published protocols. 3 retinas were pooled together to form one biological sample. Under a dissecting microscope, spring scissors were used to puncture the eye and remove the cornea, iris, and lens. The remaining eyecup had 4 radial incisions made every 90 degrees, resulting in a flat and open eye cup. The retina was then gently removed using curved tweezers and placed in a 1.5 ml microcentrifuge tube.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

1 Sample

Download data: MTX, TSV

(Submitter supplied) Age-related macular degeneration (AMD) is a chronic, multifactorial disorder and a leading cause of blindness in the elderly. Characterized by progressive photoreceptor degeneration in the central retina, disease progression involves epigenetic changes in chromatin accessibility resulting from environmental exposures and chronic stress. Here, we report that a photosensitive mouse model of acute stress-induced photoreceptor degeneration recapitulates the epigenetic hallmarks of human AMD. more...

Organism:

Mus musculus

Type:

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

Platform:

GPL13112

67 Samples

Download data: CSV

(Submitter supplied) The rapid improvements in single cell sequencing technologies and analyses methods afford greater scope for dissecting organoid cultures composed of multiple cell types and create an opportunity to interrogate these models to understand tissue biology, cellular behaviour and interactions. To this end, retinal organoids generated from human embryonic stem cells (hESCs) were analysed by single cell RNA-Sequencing at three time points of differentiation. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

79 Samples

Download data: CSV

(Submitter supplied) The addition of 5uM retinoic acid to kidney organoids at day 12 (day 7+5). This data is from the same experimental batch as data within GSE119561.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

1 Sample

Download data: MTX, TSV

(Submitter supplied) During development, distinct progenitors contribute to the nephrons versus the ureteric epithelium of the kidney. Indeed, previous pluripotent stem cell-derived models of kidney tissue either contain nephrons or pattern specifically to the ureteric epithelium. By reanalysing the transcriptional distinction between distal nephron and ureteric epithelium in human fetal kidney, we show here that while existing nephron-containing kidney organoids contain distal nephron epithelium and no ureteric epithelium, this distal nephron segment alone displays significant in vitro plasticity and can adopt a ureteric epithelial tip identity when isolated and cultured in defined conditions. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL18573 GPL24676

35 Samples

Download data: CSV, MTX, TSV, TXT

(Submitter supplied) The role of central nervous system (CNS) glia in sustaining self-autonomous inflammation and driving clinical progression in multiple sclerosis is attracting increasing scientific interest. Here, we applied a single transcription factor (SOX10)-based protocol for accelerating oligodendrocyte differentiation from human induced pluripotent stem cell (hiPSC)-derived neural precursor cells to produce three dimensional, multilineage organoids integrating submillimetric self-organizing forebrain organoids (consisting of neurons, astrocytes, oligodendrocyte precursors cells, and myelinating oligodendrocytes). more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

9 Samples

Download data: TSV

(Submitter supplied) Müller glial cells (MGs) play important roles in human retina during physiological and pathological conditions. However, there are still many obstacles to obtain large numbers of human MGs in vitro so far, which hinder the further study of MGs. Human induced pluripotent stem cells (hiPSCs) have capacity to differentiate into almost all body cells, even develop complex, organized tissues, including retinal organoids (ROs) with all cell subtypes, providing many opportunities in study of retinal development and disorders. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

15 Samples

Download data: TXT

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

Organism:

synthetic construct; Homo sapiens

Type:

Expression profiling by array; Non-coding RNA profiling by array

Platforms:

GPL19117 GPL24324

28 Samples

Download data: CEL

(Submitter supplied) Human pluripotent stem cell-derived cardiomyocytes (hPSC-CM) are a promising disease model, although hPSC-CMs are not fully mature cardiomyocytes. We examined exponential differentially expressed miRNA/gene to identify critical time-regulated transcripts associated with hPSC-CM differentiation. We uncovered 324 interactions among 29 differentially expressed genes and 51 miRNAs from 20.543 transcripts during the 120 days of hPSC-CM differentiation. more...

Organism:

synthetic construct; Homo sapiens

Type:

Non-coding RNA profiling by array

Platform:

GPL19117

14 Samples

Download data: CEL

(Submitter supplied) Human pluripotent stem cell-derived cardiomyocytes (hPSC-CM) are a promising disease model, although hPSC-CMs are not fully mature cardiomyocytes. We examined exponential differentially expressed miRNA/gene to identify critical time-regulated transcripts associated with hPSC-CM differentiation. We uncovered 324 interactions among 29 differentially expressed genes and 51 miRNAs from 20.543 transcripts during the 120 days of hPSC-CM differentiation. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL24324

14 Samples

Download data: CEL

(Submitter supplied) Global gene expression analysis of FACS-purified CD31+CD146+ vascular progenitors (VP) derived from (a) human embryonic stem cells (VP-hESC), (b) adult fibroblast derived induced pluripotent stem cells (VP-AdF-iPSC), (c) stromal primed cord blood CD34+ myeloid progenitor derived iPSC (VP-sp-CB-iPSC), (d) corresponding starting fibroblasts and myeloid progenitors, (e) human umbilical vein endothelial cells, and (f) human dermal microvascular endothelial cells.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10904

27 Samples

Download data: TXT

(Submitter supplied) Analysis of human cerebral organoids developed from both WA09 human embryonic stem cells and human urinary epithelial cell derived hiPSCs. The hypothesis tested was that organoids developed from human urinary epithelial cell derived hiPSC have similar gene expression patterns as WA09 derived organoids subjected to the same organoid development process.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

25 Samples

Download data: TXT

(Submitter supplied) Two independent induced pluripotent stem cell lines: ES4CL1 (derived from foreskin) and MR90C2 (derived from lung Fibroblast) were maintained on inactivated mouse embryonic fibroblast (MEF) feeder cells in the presence of ESC media containing DMEM, 20% knock-out serum replacement with 100ng/mL of bFGF. 7 days after seeding, cells were harvested in TrypLE Express and FACs sorted using antibodies detecting the presence of cell surface antigens GCTM-2 and CD9. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6884

24 Samples

Download data: TXT