Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

MSKCC Study 4- LARRY-barcoded pooled Knock out scRNA-seq (40KO)

ABSTRACT: This study characterizes gene knockout phenotypes of 40 genes in a human pluripotent stem cell (hPSC)-directed islet differentiation system. Samples were collected at six differentiation stages from hPSCs to SC-islet cells for scRNA-seq to examine transcriptional impact of the knockouts over time.

ORGANISM(S): Homo sapiens

PROVIDER: GSE343366 | GEO | 2026/08/12

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

MSKCC Study 2- A dual barcoding system for pooled analysis of gene knockouts in polyclonal populations (30KO)

Project description:This study characterizes gene knockout phenotypes of 30 genes in a human pluripotent stem cell (hPSC)-directed islet differentiation system. Samples were collected at six differentiation stages from hPSCs to SC-islet cells for scRNA-seq to examine transcriptional impact of the knockouts over time.

2026-08-12 | GSE343371 | GEO

MSKCC Study 1- Mapping the Temporal Impact of Perturbations on Lineage Plasticity and Gene Regulation

Project description:This study characterizes gene and enhancer knockout phenotypes of 30 genes in a human pluripotent stem cell (hPSC)-directed islet differentiation system. Samples were collected at five differentiation stages from hPSCs to SC-islet cells for scRNA-seq to examine transcriptional impact of the knockouts over time.

2025-02-03 | GSE288587 | GEO

MSKCC Study 3- A dual barcoding system for pooled analysis of gene knockouts in polyclonal populations (30KO_GEM-X)

2026-08-12 | GSE343370 | GEO

MSKCC Study 5- RNA-seq of ISL1 overexpression across different knockout genotypes during islet differentiation

Project description:This study aims to investigate the impact of ISL1 overexpression on hPSC-derived islet differentiation. hPSCs from four genotypes (WT, ISL1-/-, PDX1-/-, and PAX6-/-) were differentiated to pancreatic progenitors (day 11), transduced with ISL1-IRES2-BFP or BFP control lentivirus, and further differentiated to SC-islet (day 18). The BFP+ cells were isolated by flow cytometry sorting and subjected to RNA-seq to assess transcriptional responses to ISL1 overexpression across different genetic backgrounds.

2026-08-12 | GSE343365 | GEO

RNA-seq of ISL1 overexpression during islet differentiation.

2025-12-23 | GSE313800 | GEO

Recurrent Variations in DNA Methylation in Human Pluripotent Stem Cells and their Differentiated Derivatives [Illumina Infinium 450K DNA Methylation]

Project description:Human pluripotent stem cells (hPSCs) are potential sources of cells for modeling disease and development, drug discovery, and regenerative medicine. However, it is important to identify factors that may impact the utility of hPSCs for these applications. In an unbiased analysis of 205 hPSC and 130 somatic samples, we identified hPSC-specific epigenetic and transcriptional aberrations in genes subject to X chromosome inactivation (XCI) and genomic imprinting, which were not corrected during directed differentiation. We also found that specific tissue types were distinguished by unique patterns of DNA hypomethylation, which were recapitulated by DNA demethylation during in vitro directed differentiation. Our results suggest that verification of baseline epigenetic status is critical for hPSC-based disease models in which the observed phenotype depends on proper XCI or imprinting, and that tissue-specific DNA methylation patterns can be accurately modeled during directed differentiation of hPSCs, even in the presence of variations in XCI or imprinting. To obtain a comprehensive view of hPSC-specific epigenomic patterns, we collected 136 hESC and 69 hiPSC samples representing more than 100 cell lines for analysis. In order to establish expected variation in human tissues, we collected 80 high-quality and well-replicated samples representing 17 distinct tissue types from multiple individuals. Finally, we selected 50 additional samples from primary cell lines of diverse origin to control for any aberrations that may arise as a general, non-hPSC-specific, consequence of in vitro manipulation. With these samples, we performed genome-wide DNA methylation and mRNA expression profiling using the Illumina Infinium 27K and 450K DNA Methylation BeadChips as well as the Illumina HT12v3 Gene Expression BeadArray.

2012-05-13 | E-GEOD-31848 | biostudies-arrayexpress

Recurrent Variations in DNA Methylation in Human Pluripotent Stem Cells and their Differentiated Derivatives [Illumina HT12v3 Gene Expression]

2012-05-13 | E-GEOD-30652 | biostudies-arrayexpress

Recurrent Variations in DNA Methylation in Human Pluripotent Stem Cells and their Differentiated Derivatives [Illumina Infinium 27K DNA Methylation]

2012-05-13 | E-GEOD-30653 | biostudies-arrayexpress

Transcriptomics during the differentiation of human pluripotent stem cells to hepatocyte-like cells

Project description:Human pluripotent stem cells (hPSCs) can differentiate into all cell types in the body that may replace current cell sources applied in regenerative medicine, cell therapy, drug discovery and development and general research. Human PSC-derived hepatocyte-like cells (HLCs) have the potential to replace primary hepatocytes and other cell models applied in liver disease treatment and drug discovery and development. These cells share many features with their in vivo counterparts however, the generation of fully functional hPSC-derive HLCs is still lacking, which prevent their application in the previously mentioned fields. This study followed the transcriptome dynamics during the differentiation of hPSC-derived HLCs at definitive endoderm, hepatoblast, early HLC and late HLC developmental stages and the controls hPSCs and human liver tissues which consists of at least 70% hepatocytes. The aim is to reveal expression deviations between hPSC-derived hepatocytes and their in vivo counterparts that may contribute to the modification of differentiation protocols to generate fully functional hepatocytes.

2017-08-09 | E-MTAB-5367 | biostudies-arrayexpress

Single cell RNA-seq analysis of Induced Stem-Cell-Derived islets

Project description:The generation of pancreatic islet cells from human pluripotent stem cells (hPSCs) holds promise for cell replacement therapies for diabetes. To further analyse the characteristics of hPSC-islets and compare to primary human islets, we performed single cell RNA-seq analysis of cells sampled from cell preparation prior to transplant.

2026-02-26 | GSE268013 | 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