Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptomic features of hiPSC-derived cells with a good capability to generate retinal organoids

ABSTRACT: Transcriptomic features of hiPSC-derived cells with a good capability to generate retinal organoids

PROVIDER: PRJNA792579 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR17335800_1.fastq.gz	Fastqsanger.gz
	SRR17335800_2.fastq.gz	Fastqsanger.gz
	SRR17335801_1.fastq.gz	Fastqsanger.gz
	SRR17335801_2.fastq.gz	Fastqsanger.gz
	SRR17335802_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 180

Similar Datasets

Transcriptomic features of hiPSC-derived cells with a good capability to generate retinal organoids

Project description:Purpose: To identify transcriptomic features of hiPSC-derived cells with a good capability to generate retinal organoids Methods: Human induced pluripotent stem cell (hiPSC) samples were collected at two time points for RNA sequencing (day zero and seven, each time point in triplicate). Cell pellets were collected and flash frozen. Total RNA was extracted by a phenol/chloroform method using TRIzol LS reagent (ThermoFisher Scientific, MA) according to the manufacturer's guidelines. tRNA was treated with DNAse I prior to library preparations being performed for RNAsequencing. Results: Human iPSC lines show variation in their ability to differentiate into a neuroectodermal/early eye field phenotype. This study identified a panel of signature transcripts that were differentially expressed at seven days of differentiation, between lines of low- and high-retinal propensity. Conclusions: This study provides a gene profile that identifies which hiPSC-derived cells have a good capability to generate retinal organoids. This allows for the analysis of retinal propensity by quantitative PCR within the first seven days of differentiation.

2023-06-21 | GSE192665 | GEO

Exon array analysis for SFEBq differentiation-defective clones and good clones

Project description:It remains controversial whether human induced pluripotent stem cells (hiPSCs) are distinct from human embryonic stem cells (hESCs) in their molecular signatures and differentiation properties. We examined the gene expression and DNA methylation of 49 hiPSC and 10 hESC lines and identified no molecular signatures that distinguished hiPSCs from hESCs. Comparisons of the in vitro directed neural differentiation of 40 hiPSC and four hESC lines showed that most hiPSC clones were comparable to hESCs. However, in seven hiPSC clones, significant amount of undifferentiated cells persisted even after neural differentiation and resulted in teratoma formation when transplantated into mouse brains. These differentiation-defective hiPSC clones were marked by higher expression of several genes, including those expressed from long terminal repeats of human endogenous retroviruses. These data demonstrated that many hiPSC clones are indistinguishable from hESCs, while some defective hiPSC clones need to be eliminated prior to their application for regenerative medicine. We extracted total RNA from 3 differentiation-defective clones, 3 good clones and 2 somatic cells, and hybridized them to Affymetrix exon arrays.

2013-12-03 | E-GEOD-42449 | biostudies-arrayexpress

Expression data from human induced pluripotent stem cells derived retinal pigment epithelium (hiPSC-RPE)

Project description:We generated hiPSCs from patients fibloblast with retinitis pigmentosa (RP) using retrovirus and Sendai virus vectors, which we differentiated into hiPSC derived retinal pigment epithelium using two different methods (SDIA and SFEB methods). We investigated whether these hiPSC-RPE colonies, which were differentiated from various cell lines and methods, showed similar gene expression patterns to those of native RPE. We classified hiPSC-RPE, hiPSCs, and fibroblasts from RP patients, hRPE (commercially available human fetal RPE, Lonza) , ARPE19 (a human RPE cell line), and other human tissues from 54,675 probe sets using microarray data.

2014-11-03 | E-GEOD-50738 | biostudies-arrayexpress

Reliability of human retinal organoid generation from hiPSC-derived neuroepithelial cysts

Project description: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. Here, we tested seven different hiPSC lines, which reproducibly generated HROs. Histologic and ultrastructural analyses support regulated HRO differentiation and maturation. The different hiPSC lines appeared to be a larger source of variance than experimental rounds. Whereas previous reports showed that HRO in several other protocols contain a rather low numbers of cones compared to rods, HROs derived by the cyst protocol consistently are cone-richer and with an comparable ratio of cones, rods, and Müller glia. Additionally, we devised a potential strategy to systematically evaluate different protocols side-by-side through parallel differentiation from the same hiPSC batches: The cyst-protocol was compared to a conceptually different protocol based on cell aggregate formation from single hiPSCs. Comparison of four hIPSC lines showed that both protocols reproduced key characteristics of retinal epithelial structure and cell composition, but the cyst-protocol provided a higher HRO yield. Further, while cyst-derived HROs maintained stable at least up to date 250, whereas single hiPSC-derived HROs showed spontaneous pathologic changes already by day 200. Overall, our data provide insight into the efficiency, reproducibility, and stability of the cyst-protocol for HRO generation, which will be useful for further organoid system optimization, as well as basic and translational research applications.

2023-09-26 | GSE237007 | GEO

Transcriptome analysis of single cell-derived hiPSC-lt-NES cell clones

Project description:To identify cell-populations within human iPSC-derived long-term self-renewing neural epithelial stem cells (hiPSC-lt-NES cells) which retain capacities to generate undesired grafts, we established single cell-derived hiPSC-lt-NES cell clones and performed gene expression microarray analysis.

2023-06-04 | GSE166051 | GEO

Transcriptome analysis of hiPSC derived lt-NES cells

2023-06-04 | GSE225719 | GEO

Expression data from human induced pluripotent stem cells derived retinal pigment epithelium (hiPSC-RPE)

2014-11-03 | GSE50738 | GEO

Investigating hiPSC-CMs_DongLi

Project description:Proteomic analysis of hiPSC-CMs with drug treatment

2021-05-01 | MSV000087351 | MassIVE

Rapid and efficient generation of myelinating oligodendrocytes from human induced pluripotent stem cells using a combination of three transcription factors [hiPSC]

Project description:We demonstrate that the induction of three transcription factors (SOX10, OLIG2, NKX6.2) in hiPSC-derived neural progenitor cells (hiPSC-NPC) is sufficient to rapidly generate O4+ oligodendrocytes with an efficiency of 60 to 70% within 28 days.

2017-03-06 | GSE79912 | GEO

Expression profiling in hiPSC-derived liver sinusoidal endothelial cells and hepatic stellate cells

Project description:We have established culture systems to generate liver sinusoidal endothelial cells (LSECs) and hepatic stellate cells (HSCs) from hiPSCs. To characterize gene expression profiling in hiPSC-derived LSECs and HSCs, transcriptome analysis was performed.

2017-07-27 | GSE92771 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data