12a62e42-0dc8-4c7b-af1d-c249c0689b02 - samples
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ABSTRACT:
PROVIDER: EGAD00001005933 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:Fastq files of mRNA-seq data of induced pluripotent stem cells (iPSC), definitive endoderm (DE) and hepatocyte-like cells (HLC). The dataset comprises data from the in vitro differentiation protocol Cellartis (Takara Bio, "CEL", n = 4) and several interventions (11x3 replicates).
| EGAD00001005935 | EGA
Project description:Fastq files of ATAC-seq data of induced pluripotent stem cells (iPSC), definitive endoderm (DE), hepatocyte-like cells (HLC) and primary human hepatocytes (PHH).
The dataset comprises data from two different in vitro differentiation protocols: Cellartis (Takara Bio, "CEL", n = 4) and as described by Wang et al. (PMID: 28287600, "HAY", n = 1), as well as from 3 PHH donors.
| EGAD00001005934 | EGA
Project description:Fastq files of deeply sequenced single cell RNA-seq data (Smartseq2, approx. 2 million reads / sample) of hepatocyte-like cells (HLC) and primary human hepatocytes (PHH).
The dataset comprises data from two different in vitro differentiation protocols: Cellartis (Takara Bio, "CEL", n = 3) and as described by Wang et al. (PMID: 28287600, "HAY", n = 1), as well as PHH from 3 donors. Each replicate comprises 96 single cells.
| EGAD00001005946 | EGA
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
Project description:The differentiation of pluripotent stem cells to hepatocyte-like cells offers the perspective of unlimited supply of human hepatocytes. However, the degree of differentiation of hepatic-like cells (HLC) remains controversial. To obtain an unbiased characterization, we performed a transcriptomics study using the Affymetrix Gene Chip® HG-U133 plus 2.0, with HLC derived from embryonic and induced stem cells (ESC, hiPSC) from two different laboratories. Genome-wide gene expression profiles of ESC and HLC were compared to freshly isolated and up to 14 days cultivated primary human hepatocytes (see submission E-MTAB-3994) obtained under patient informed consent from three male donors. Three biological replicas were used for each ESC and HLC models. (associated data set: E-MTAB-3994 - Gene expression profile of human embryonic stem cell-derived hepatocyte-like cells in matrigel and recombinant laminins)
2016-02-24 | E-MTAB-4442 | biostudies-arrayexpress
Project description:During embryonic development bipotential hepatoblasts differentiate into hepatocytes and cholangiocytes- the two main cell types within the liver. Cell fate decision depends on elaborate interactions between distinct signalling pathways, namely Notch, WNT, TGFβ, and Hedgehog. Several in vitro protocols have been established to differentiate human pluripotent stem cells into either hepatocyte or cholangiocyte like cells (HLC/CLC) to enable disease modelling or drug screening. During HLC differentiation we observed the occurrence of epithelial cells with a phenotype divergent from the typical hepatic polygonal shape- we refer to these as endoderm derived epithelial cells (EDECs). These cells do not express the mature hepatocyte marker ALB or the progenitor marker AFP. However they express the cholangiocyte markers SOX9, OPN, CFTR as well as HNF4α, CK18 and CK19. Interestingly, they express both E Cadherin and Vimentin, two markers that are mutually exclusive, except for cancer cells. EDECs grow spontaneously under low density cell culture conditions and their occurrence was unaffected by interfering with the above mentioned signalling pathways.
2018-06-30 | GSE116455 | GEO
Project description:SVF was isolated from ABD and GF-adipose tissue biopsies by collagenase digestion and centrifugation, from 5 healthy women (38yo ±4.4; 31.8kg/m-2 ±3.12; WHR 0.86 ±0.05). After isolation, cells were counted with a Countess II automated cell counter (Thermofisher Scientific). Single cell suspension (56K/mL) was distributed into eight wells of a 384-well source plate (Takara Bio USA, San Jose, CA) and dispensed onto a iCELL8 350v Chip (Takara Bio USA) using an iCELL8 MultiSample NanoDispenser (Takara Bio USA). We distributed the ABD and GF-SVF of each subject on the same chip. The method used was described in [6]. In brief, mRNA from single cells were isolated, converted to full-length cDNA prior to unbiased amplification of 3’ and 5’ ends using SMART-Seq® ICELL8® Application Kit (Takara Bio, USA). Multiplexed sequencing libraries were generated from cDNA using the Illumina Nextera XT protocol and 150bp paired-end sequencing was performed on an Novogene HiSeqX instrument.
2024-02-23 | GSE255996 | GEO
Project description:Hepatocyte-like cells differentiated from human iPS cells are expected to be utilized in pharmaceutical research and regenerative medicine. Recently, various culture methods for human iPS cell maintenance have been developed. However, it is not well known whether human iPS cell maintenance method affects hepatic differentiation potency. In this study, we cultured human iPS cells using four maintenance methods: ReproStem medium with feeder cells (mouse embryonic fibroblasts), AK02N medium with iMatrix-511 (E8 fragments of laminin511), Essential 8 medium with Vitronectin N (N-terminal domain of vitronectin), TeSR-E8 medium with Vitronectin XF (xeno-free vitronectin). Then, these human iPS cells were differentiated into the hepatocyte-like cells. Interestingly, the gene expression levels of definitive endoderm markers in the definitive endoderm cells generated from human iPS cells cultured with ReproStem or TeSR-E8 medium were higher than those in other groups. The gene expression level of foregut marker, HHEX, in the definitive endoderm cells generated from human iPS cells cultured with ReproStem medium was higher than that in other groups. Consistently, the expression levels of hepatocyte markers, albumin and urea secretion capacity, and CYP3A4 activity in the hepatocyte-like cells generated from human iPS cells cultured with ReproStem medium were higher than those in other groups. Our data indicated that the most suitable human iPS cell maintenance method for efficient hepatic differentiation was the on-feeder method which uses mouse embryonic fibroblasts, but not feeder-free methods. In conclusion, human iPS cell maintenance method largely affects hepatic differentiation potency.
2018-09-25 | GSE119698 | GEO
Project description:We evaluated the hepatic developmental toxicity of TBBPA/TBBPS/TCBPA with a human embryonic stem cells (hESC) system. We found that TBBPA/TBBPS/TCBPA might adversely affect human hepatocyte-like cells specification from hESCs via mainly impairing definitive endoderm specifications, suggesting the early stages of embryonic development are susceptible to the three compounds.
2020-04-29 | GSE129412 | GEO
Project description:To understand in detail the molecular phases that occur during the differentiation of human embryonic stem cells to hepatocyte-like cells we performed an RNA-seq time course of the stages of differentiation across the 21 day differentiation time course. We used a chemically defined (serum-free) protocol, modified from Si-Tayeb et al., 2010 and Song et al., 2009. We describe acquisition of definitive endoderm characteristics at day 3, followed by hepatoblast charcter at day 7-13 and then maturation to hepatocyte-like cells at day 21. Time course of differentiation of human embryoic stem cells to hepatocyte-like cells over 21 days, using an adapted chemically defined protocol of Song et al., 2009; Cell Research
2017-04-28 | E-GEOD-70741 | biostudies-arrayexpress