Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptomic analysis of corticosteroids-treated hiPSC-derived RPE cells

ABSTRACT: Transcriptomic analysis of corticosteroids-treated hiPSC-derived RPE cells

PROVIDER: PRJNA723495 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR14293000_1.fastq.gz	Fastqsanger.gz
	SRR14293000_2.fastq.gz	Fastqsanger.gz
	SRR14293001_1.fastq.gz	Fastqsanger.gz
	SRR14293001_2.fastq.gz	Fastqsanger.gz
	SRR14293002_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 30

Similar Datasets

Transcriptomic analysis of corticosteroids-treated hiPSC-derived RPE cells

Project description:The aim of this study was to analyze the pan-transcriptional regulations induced in hiPSC-derived RPE (iRPE) cells by corticoids with specific inhibitors of their receptors to decipher specific genes regulated by MR or GR activation. Cells were seeded at P3 in cell culture plastic dishes. On day 35, one week prior to corticosteroids treatments, RDMw/oA medium was remove and iRPE cells were incubated in experimental corticosteroid-free medium (DMEM, high glucose, HEPES, no phenol red, 10% Fetal Bovine Serum, charcoal stripped). On day 42, iRPE cells were treated for 24 h with the following corticosteroids treatments: aldosterone (10-7 M), cortisol (10-7 M) and cortisol (10-7 M) plus RU-486 (10-5 M). As corticosteroids were dissolved in ethanol (EtOH) or methanol (MeOH) control cells were treated with 0.1% EtOH or MeOH in medium. Total RNA samples extracted from iRPE were sequenced at the iGenSeq transcriptomic platform of the Brain and Spine Institute (ICM, Paris, France). RNA quality was checked by capillary electrophoresis (Agilent 2100 Bioanalyzer system) and RNA with integrity numbers (RIN) ranging from 7.8 to 8.2 was accepted for library generation. Quality of raw data has been evaluated with FastQC. Librairies were prepared with Roche KAPA mRNA HyperPrep kit and sequenced with the Illumina NextSeq 500 Sequencing system using NextSeq 500 High Output Kit v2 (150 cycles), 400 millions of reads, 50Gbases. Star v2.5.3a has been used to align reads on reference genome hg19 using standard options. Quantification of gene and isoform abundances has been done with rsem 1.2.28, prior to normalization on library size with edgeR bioconductor package. Finally, differential analysis has been also conducted with edgeR. Multiple hypothesis adjusted p-values were calculated with the Benjamini-Hochberg procedure to control FDR. We identified genes differentially regulated by MR and GR, and those regulated by both MR and GR activation in hiPSC-RPE cells.

2021-09-06 | GSE172478 | GEO

Expression data for hiPSC-derived RPE treated with 10mM Nicotinamide or vehicle

Project description:We did the RNA-seq analysis to examine the global impact of Nicotinamide (NAM) on hiPSC-derived RPE transcriptome in order to better understand the mechanism of action of NAM. NAM inhibited the expression of Age related Macular degeneration (AMD) associated protein transcripts in hiPSC-derived RPE.

2017-01-25 | GSE90889 | GEO

Expression data for hiPSC-derived RPE treated with 10mM Nicotinamide or vehicle

Project description:Nicotinamide (NAM) inhibited the expression of Age related macular degeneration (AMD) associated proteins in hiPSC-derived retinal pigment epithelium (RPE). We did the microarray analysis to examine the global impact of NAM on hiPSC-derived RPE transcriptome in order to better understand the mechanism of action of NAM.

2018-01-15 | GSE76923 | GEO

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

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

2014-11-03 | GSE50738 | GEO

scRNA-seq of siRNA treated hiPSC-derived islet cells

Project description:scRNA-seq of siRNA treated hiPSC-derived islet cells

2023-09-11 | GSE218547 | GEO

Transcriptomic effects of prenatal exposure to corticosteroids on synaptic transmission

Project description:Prenatal exposure to synthetic corticosteroids can significantly alter postnatal development through changes in neurotransmitters and their receptors, and thus having long-lasting behavioral effects. Some of these changes have been observed in animal experiments, others also in humans prenatally exposed to synthetic corticosteroids. Here, we focused on transcriptomic changes within the prefrontal cortex of female rats prenatally exposed to either betamethasone or saline. The transcriptome has been assessed by novel computational tools to determine complex changes that may have life-long effects on phenotype, i.e., behavior. We analyzed how composition, topology and modulatory networks of the genomic fabric of the dopaminergic, GABAergic, and glutamatergic synapse (the transcriptome of the most interconnected and stably expressed gene network responsible for specific transmission) are affected by prenatal exposure to corticosteroids and postnatal ketamine/saline treated NMDA-induced seizures.

2016-01-09 | GSE76694 | GEO

TMT-MS of PCIF1 siRNAs treated RPE-1 cells

Project description:RPE-1 cells treated with the indicated siRNAs for 48 h were subjected to the tandem mass tag quantitative proteomics analysis.Carry out relative protein quantification analysis using tandem mass tag mass spectrometry in RPE-1 cells to investigate the mechanism underlying PCIF1 attenuates ciliation.

2024-03-21 | PXD044338 | Pride

scRNA-seq of siRNA treated hiPSC-derived islet cells

Project description:scRNA-seq of siRNA treated hiPSC-derived islet cells

| PRJNA904286 | ENA

Transcriptomic effects of prenatal exposure to corticosteroids on synaptic transmission

Project description:Prenatal exposure to synthetic corticosteroids can significantly alter postnatal development through changes in neurotransmitters and their receptors, and thus having long-lasting behavioral effects. Some of these changes have been observed in animal experiments, others also in humans prenatally exposed to synthetic corticosteroids. Here, we focused on transcriptomic changes within the prefrontal cortex of female rats prenatally exposed to either betamethasone or saline. The transcriptome has been assessed by novel computational tools to determine complex changes that may have life-long effects on phenotype, i.e., behavior. We analyzed how composition, topology and modulatory networks of the genomic fabric of the dopaminergic, GABAergic, and glutamatergic synapse (the transcriptome of the most interconnected and stably expressed gene network responsible for specific transmission) are afected by the prenatal exposure to corticosteroids and postnatal ketamine-induced seizures. One sex (F) x two prenatal exposures (B = betamethasone, S = saline) x two postnatal treatments (K = ketamine, S = saline). Biological replicates: 4 FSS, 4 FBS, 4 FBK.

2016-01-09 | E-GEOD-76694 | biostudies-arrayexpress

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