Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Characterization of Definitive Endoderm formation from HESC and iPSC lines by Microarray analysis

ABSTRACT: HESC-H9 and iPSC lines 3.5, 3.6 and 3.12 were analyzed using Affymetrix microarray before and after Definitive Endoderm (DE) formation. DE was induced using the ActivinA differentiation protocol described by D'Amour et al., 2006 (PMID: 16258519) Clustering analysis of transcripts that were differentially regulated during DE formation indicated that iPSC lines 3.5 and 3.12 differentiate in manner that is highly similar to HESC-H9 cells iPSC line 3.6 had a more divergent transcriptional profile.

ORGANISM(S): Homo sapiens

PROVIDER: GSE25557 | GEO | 2010/12/25

SECONDARY ACCESSION(S): PRJNA134277

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Characterization of Definitive Endoderm formation from HESC and iPSC lines by Microarray analysis

Project description:HESC-H9 and iPSC lines 3.5, 3.6 and 3.12 were analyzed using Affymetrix microarray before and after Definitive Endoderm (DE) formation. DE was induced using the ActivinA differentiation protocol described by D'Amour et al., 2006 (PMID: 16258519) Clustering analysis of transcripts that were differentially regulated during DE formation indicated that iPSC lines 3.5 and 3.12 differentiate in manner that is highly similar to HESC-H9 cells iPSC line 3.6 had a more divergent transcriptional profile. Three induced pluripotent stem cell lines (iPSC) and one human embryonic stem cell line (hESC - H9) were collected as undifferentiated (UD) cells, and flash frozen. These cell lines were also subjected to definitive endoderm (DE) induction, collected and flash frozen. RNA was harvested from the frozen cell pellets and hybridized to the Affymetrix microarray chip. The three iPSC cell lines are iPSC 3.5, iPSC 3.6. and iPSC 3.12. In the UD state, iPSC 3.5 was analyzed in duplicate, while iPSCs 3.6 and 3.12 and H9s were analyzed in biological triplicate. All four cell lines were analyzed as biological triplicates for DE induction.

2010-12-25 | E-GEOD-25557 | biostudies-arrayexpress

Synergism between Activin A and BMP4 in directing the formation of definitive endoderm in human embryonic stem cells

Project description:Human embryonic stem cells (HESCs) herald tremendous promise for the production of clinically useful cell types for the treatment of injury and disease. Numerous reports demonstrate their differentiation into definitive endoderm (DE) cells, the germ layer from which pancreatic β cells and hepatocytes arise, solely from exposure to a high dose of recombinant Activin/Nodal. Here, we show that combining a second related ligand, BMP4, in combination with Activin A yields 15 to 20% more DE as compared to Activin A alone. The addition of recombinant BMP4 accelerates the downregulation of pluripotency factors, particularly SOX2, and results in upregulation of endogenous BMP2 and BMP4, which in turn leads to elevated levels of phospho-SMAD1/5/8 over the next three days of differentiation. Combined Activin A and BMP4 treatment also leads to an increase in the expression of DE genes CXCR4, SOX17 and FOXA2 when compared to Activin A addition alone. Comparative microarray studies between DE cells harvested on day 3 of differentiation further reveal a novel set of genes upregulated in response to initial BMP4 exposure. Several of these, including APLNR, LRIG3, MCC and LZTS1, are expressed either in the mouse primitive streak, the site of DE formation, or in nascent DE itself. Thus, this synergism between Activin A and BMP4 during the in vitro differentiation of HESC into DE suggests a complex interplay between BMP and Activin/Nodal signaling during the in vivo allocation and expansion of the endoderm lineage. 3 biological replicates of 3-day ActivinA treated HES3 human stem cell culture were compared to 3-day ActivinA+Bmp4 treated HES3 human stem cell culture and observed for differential genes expression

2011-11-10 | E-GEOD-30630 | biostudies-arrayexpress

MicroRNA expression data from differentiation of human H9 ESCs into definitive endoderm on MEF feeder layers

Project description:Pluripotent hESCs can differentiate into the three primary embryonic lineages (endoderm, mesoderm, ectoderm) as well as extraembryonic tissues. Definitive endoderm (DE) is the first step into the pathway to endoderm dreived tissues (pancreas, liver, gut, lung). We used microarrays to detail the changes in microRNA expression during the transition from pluripotent hESCs into definitive endoderm. hESCs (H9) were differentiated in the presence of Activin A and Wnt3A under low serum conditions to induce DE formation. Samples were collected at day 0 (hESCs), and day 4 (DE).

2010-07-30 | E-GEOD-16689 | biostudies-arrayexpress

Global gene expression analysis of pluripotent cell lines and corresponding starting donor source cells

Project description:Global gene expression analysis of induced pluripotent stem cell lines and their corresponding source cells Total RNA was harvested from H9 hESC (P51), non-integrated episomal CB-iPSC clones 6.2, 6.11, 6.13, (P14), 19.11, (P11), nonviral KER-iPSC clones KA.1, KA.3 (P13) nonviral FFB-iPSC: F.1, F.6 (P14) and viral fibroblast iPSC clones IMR1 (P66), IMR4 (P64). A single sample of each condition was used for this analysis.

2012-08-23 | E-GEOD-35028 | biostudies-arrayexpress

Global gene expression in patient keratinocytes and patient-specific iPS-derived keratinocytes

Project description:Patients with recessive dystrophic epidermolysis bullosa (RDEB) lack functional Type VII collagen and suffer severe blistering and chronic wounds that ultimately lead to infection and development of lethal squamous cell carcinoma (SCC). The discovery of induced pluripotent stem cells (iPSCs) and the ability to edit the genome bring the possibility to provide definitive genetic therapy through corrected autologous tissues. We have formed a multidisciplinary team with the ultimate goal to develop an iPSC-based therapy for RDEB. Here, we present a clinical protocol that generates autologous, corrected epithelial keratinocyte sheets with the COL7A1 gene mutation corrected for grafting on to patients. We demonstrate the utility of sequential reprogramming and novel adenovirus-associated viral genome editing to generate corrected iPSC banks. iPSC-derived keratinocytes were produced with minimal heterogeneity and secreted wild-type collagen VII, resulting in stratified epidermis in vitro and in vivo in mice. Sequencing of corrected cell lines prior to tissue formation revealed heterogeneity of SCC-predisposing mutations, allowing us to select COL7A1 corrected banks with minimal mutational burden for downstream epidermis production. Our results provide a first clinical platform to use iPSCs in the treatment of debilitating genodermatoses. Microarray analysis of iPS-derived keratinocytes from two RDEB patients (iPS-K1 and iPS-K3), corresponding patient keratinocytes (AHK1 and AHK2), normal human keratinocytes (NHK), as well as H9 human embryonic stem cells (hESC - H9). All samples were analyzed in duplicate and differential gene expression was measured relative to H9.

2014-11-26 | E-GEOD-63101 | biostudies-arrayexpress

BRACHYURY knockdown in differentiating hESCs

Project description:Transcriptional profiling of H9 hESCs (wild type and BRACHYURY shRNA knockdown) differentiated for 36h or 72h in chemically-defined culture media supplemented with FGF2, LY294002 and either BMP4 or ActivinA.

2015-05-19 | E-MTAB-2912 | biostudies-arrayexpress

Transcriptional and epigenetic profiling of EP-derived iPSCs (RNASeq)

Project description:We generated 20 iPSC lines from erythroid precursors (EP) and compared them to 3 lines derived from dermal fibroblasts (DF), H9 hESC, four precursor EP populations and one precursor DF population. This experiment describes the RNASeq profiling of those samples performed in order to QC the lines. These Human samples are not consented for release of identifiable sequencing data, so processed RNASeq counts are provided.

2014-09-01 | E-MTAB-2710 | biostudies-arrayexpress

Transcriptional and epigenetic profiling of EP-derived iPSCs (RRBS)

Project description:We generated 20 iPSC lines from erythroid precursors (EP) and compared them to 3 lines derived from dermal fibroblasts (DF), H9 hESC, four precursor EP populations and one precursor DF population. This experiment describes the RRBS profiling of those samples performed in order to QC the lines. These Human samples are not consented for release of identifiable sequencing data, so processed methylation calls over CpG islands are provided.

2014-09-01 | E-MTAB-2711 | biostudies-arrayexpress

Different propensity in hematopoietic differentiation potential among distinct human pluripotent stem cell lines

Project description:Lineage-specific differentiation potential varies among different human pluripotent stem cell (hPSC) lines. A stem cell bank may advice researchers on which hPSCs exhibit the highest differentiation potential for a certain lineage. In this study, we aimed at characterizing the hematopoietic differentiation potential from 14 hESC/iPSC lines through the embryoid body (hEB) differentiation system. We carried out gene expression profiling on six different hESC lines grouped according to their ability to differentiate towards hematopoietic lineage: SHEF1, AND1 and H1 were considered as good (high CD45 expression and high CFU potential), whereas H9, HS181 and VAL3 were selected as poor-blood differentiating lines (low CD45 expression and low CFU potential). Human ESC samples were collected during the exponential cell growth phase and stabilized in RNA later. 500 ng of each total RNA sample was labelled with Cy3 using the Quick-Amp Labelling kit and hybridized with the Gene Expression Hybridization kit to a Whole Human Genome Oligo Microarray (Agilent Technologies) following the Manufacturer’s instructions. Each cell line was analyzed as independent duplicates. H9 hESC line was used as the baseline.

2010-07-24 | E-GEOD-23091 | biostudies-arrayexpress

Analysis of the protein cargo of extracellular vesicles isolated from cultured line H9 human stem cells

Project description:Extracellular vesicles (EV) are secreted by nearly every mammalian cell type and contain a wealth of bioactive cargo capable of modulating target cell physiology and function though a variety of paracrine signaling mechanisms (Leavitt et al., 2019). Human embryonic stem cell (hESC)-derived extracellular vesicles (hESC-derived EV), were extracted from the hESC line H9 (WA09 Wicell Research Institute, Inc., Madison, WI). We analyzed the bioactive protein cargo to identify components that help to resolve radiation-induced injury to the lung in mice when injected in vivo.

2021-02-24 | PXD023213 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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