GEO DataSets

Analysis of H9 (WAO9) embryonic stem (ES) cells subjected to hepatic differentiation protocol. ES-derived hepatocytes depleted of nuclear hormone receptor HNF4A also examined. Results provide insight into the role of HNF4A during the formation of hepatocytes from pluripotent stem cells.

Organism:

Homo sapiens

Type:

Expression profiling by array, count, 4 development stage, 2 genotype/variation, 4 time sets

Platform:

GPL570

Series:

GSE25417

12 Samples

Download data: CEL, CHP

(Submitter supplied) The availability of pluripotent stem cells offers the possibility of using such cells to model hepatic disease and development. With this in mind, we previously established a protocol that facilitates the differentiation of both human embryonic stem cells and induced pluritpotent cells into cells with hepatocyte characteristics. The use of highly defined culture conditions and the avoidance of feeder cells or embryoid bodies allowed synchronous and reproducible differentiation to occur. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS3926

Platform:

GPL570

12 Samples

Download data: CEL, CHP

(Submitter supplied) Understanding gene expression profile and transcriptional regulation of healthy adult human hepatocytes Gene expression was analyzed

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

9 Samples

Download data: CEL, CHP

(Submitter supplied) Gene expression profile analysis allowed to identify a panel of genes and pathways characteristic of hESC-and HepaRG-derived cholangiocytes.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL14550

28 Samples

Download data: TXT

(Submitter supplied) Human induced hepatic lineage-oriented stem cells (hiHSCs) can be established as a new type of human induced pluripotent stem cells (hiPSCs) with only some modifications of their culture conditions in both generation and self-renewal. hiHSCs were generated and expanded at a very high density under non-typical coculture with feeder cells in a chemically defined hiPSC medium . In detail, hiHSCs were generated from human non-hepatic cells by gene transfer with pantropic retrovirus vectors carrying the three transcription factor genes OCT3/4, SOX2, and KLF4. more...

Organism:

Homo sapiens

Type:

Expression profiling by array; Third-party reanalysis

Platform:

GPL6480

5 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

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

Platforms:

GPL11154 GPL15207

28 Samples

Download data: BED, CEL

(Submitter supplied) HNF4a has been shown to be critical for hepatocyte differentiation from iPS cells.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

2 Samples

Download data: BED

(Submitter supplied) HNF4a has been shown to be a central regulator of hepatocyte differentiation and function in adult mice. It was recently shown the HNF4a regulates the onset of hepatic gene expression during liver differentiation in vitro and is critical for the specification of liver towards a hepatic fate We examined the global gene expression of the differentiaiton of iPS cells into specified hepatic cells on consecutive days of liver differentiation (Mallanna et al 2013) to determine the onset of hepatic gene expression and the role HNF4a plays during hepatic specification.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL15207

26 Samples

Download data: CEL, TXT

(Submitter supplied) Human pluripotent stem cells (hPSCs) offer a unique cellular model to study lineage specifications of the primary germ layers during human development. We profiled single-cell RNA-seq (scRNA-seq) on four lineage-specific progenitor cells derived from hESCs. Our scRNA-seq analyses revealed each type of progenitors display various extend of heterogeneity. Specifically, definitive endoderm cells (DECs) not only show a greater degree of heterogeneity, but are also enriched in metabolic signatures. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

1810 Samples

Download data: CSV

(Submitter supplied) The gene expression profiles of differentiating human pluripotent stem cells (hPSCs) were analyzed by DNA microarray. We identified differences and commonalities among six human pluripotent stem cell lines: the hESCs KhES1, KhES2, KhES3, and H1, and the iPSCs 201B7 and 243G1. Analysis of DNA microarray data suggested that hepatocyte-like differentiation of EBs treated with ammonia in Lanford medium.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL14550

24 Samples

Download data: TXT

(Submitter supplied) Pluripotent stem cells are being actively studied as a cell source for regenerating damaged liver. For long term survival of engrafting cells in the body, not only do the cells have to execute liverspecific function but also withstand the physical strains and invading pathogens. The cellular innate immune system orchestrated by the interferon (IFN) pathway provides the first line of defense against pathogens. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

12 Samples

Download data: TXT

(Submitter supplied) Plasticity of differentiated cells has been proved by nuclear transfer, induced pluripotent cells and transdifferentiation. Here we show that by transduction of 3 factors (Hnf1alpha, Gata4, and Foxa3) and p19Arf inactivation, tail-tip fibroblasts can be converted to hepatocyte-like (iHep) cells, expressing hepatocyte marker genes, and acquiring many mature hepatocyte functions in vitro and in vivo.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL4134

13 Samples

Download data: TXT

(Submitter supplied) HNF4a and FOXA2 are two liver enriched transcription factors that have been shown capable of reprogramming fibroblasts into hepatocyte-like cells. However to date it is not yet understood how these master regulators, expressed in both embryonic and adult liver contribute to the transcriptional changes necessary for hepatocyte maturation during development. Consequently we undertook to identify binding sites and target genes for HNF4a and FOXA2 in the embryonic liver. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9185

3 Samples

Download data: BED, BIGWIG, WIG

(Submitter supplied) Here, we developed a new differentiation protocol by mimicking the two-stage development of hepatoblasts to potentiate their transition to hepatic progenitor cells (hiHPCs), which permits the high-efficiency generation of hiHPCs from chemically induced pluripotent stem cells (hCiPSCs). Moreover, hCiPSC-derived hiHPCs can further differentiate into mature hepatocytes (hiHEPs). We use single-cell RNA sequencing (scRNA-seq) to analyze the two-stage of hepatoblasts indicating the similarity between hepatoblasts differentiated in vitro and in vivo. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

16 Samples

Download data: MTX, TSV, TXT

(Submitter supplied) Conventional 2-D differentiation from pluripotency fails to recapitulate cell interactions occurring during organogenesis. 3-D organoids generate complex organ-like tissues, however it is unclear how heterotypic interactions impact lineage identity. Here we use single-cell RNA-seq to reconstruct hepatocyte-like lineage progression from pluripotency in 2-D culture. We then derive 3-D liver bud (LB) organoids by reconstituting hepatic, stromal, and endothelial interactions, and deconstruct heterogeneity during LB development. more...

Organism:

Mus musculus; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL16791 GPL17021

741 Samples

Download data: CSV

(Submitter supplied) Conventional 2-D differentiation from pluripotency fails to recapitulate cell interactions occurring during organogenesis. 3-D organoids generate complex organ-like tissues, however it is unclear how heterotypic interactions impact lineage identity. Here we use single-cell RNA-seq to reconstruct hepatocyte-like lineage progression from pluripotency in 2-D culture. We then derive 3-D liver bud (LB) organoids by reconstituting hepatic, stromal, and endothelial interactions, and deconstruct heterogeneity during LB self-organization. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

770 Samples

Download data: CSV

(Submitter supplied) The winged helix transcription factor Foxl1 is a marker for progenitor cells and their descendants in the mouse liver in vivo. Here, we purify progenitor cells from Foxl1-Cre; RosaYFP mice and evaluate their proliferative and differentiation potential in vitro. Treatment of Foxl1-Cre; RosaYFP mice with 3,5-diethoxycarbonyl-1,4-dihydrocollidine diet led to an increase of the percentage of YFP-labeled Foxl1+ cells. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platforms:

GPL4134 GPL10333

43 Samples

Download data: TXT

(Submitter supplied) The winged helix transcription factor Foxl1 is a marker for progenitor cells and their descendants in the mouse liver in vivo. Here, we purify progenitor cells from Foxl1-Cre; RosaYFP mice and evaluate their proliferative and differentiation potential in vitro. Treatment of Foxl1-Cre; RosaYFP mice with 3,5-diethoxycarbonyl-1,4-dihydrocollidine diet led to an increase of the percentage of YFP-labeled Foxl1+ cells. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL10333

17 Samples

Download data: TXT

(Submitter supplied) The winged helix transcription factor Foxl1 is a marker for progenitor cells and their descendants in the mouse liver in vivo. Here, we purify progenitor cells from Foxl1-Cre; RosaYFP mice and evaluate their proliferative and differentiation potential in vitro. Treatment of Foxl1-Cre; RosaYFP mice with 3,5-diethoxycarbonyl-1,4-dihydrocollidine diet led to an increase of the percentage of YFP-labeled Foxl1+ cells. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL4134

26 Samples

Download data: TXT

(Submitter supplied) Purpose: To investigate the impact of MODY1/HNF4A mutation on foregut development using differentiated control and MODY1-hiPSCs Methods: RNA-Seq was performed on foregut/hepato-pancreatic progenitors obtained on day 14 of the directed differentiation of hiPSCs from MODY1 patients (3 clones from iN904-1, 1 clone from iN904-2) and family controls (3 clones from iN904-7, 2 clones from iN904-13). Differential expression analysis, KEGG pathway and gene ontology analyses were carried out. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

9 Samples

Download data: TSV, TXT, XLSX