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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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MicroRNA expression data from differentiation of human Cyt49 ESCs into definitive endoderm in feeder-free conditions

ABSTRACT: Pluripotent hESCs can differentiate into the three primary embryonic lineages (endoderm, mesoderm, ectoderm) as well as extraembryonic tissues. Definitive endoderm 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 (Cyt49) were differentiated in the presence of Activin A and Wnt3A under low serum conditions to induce DE formation. Samples were collected at day 0 (2 samples), day 2 (3 samples) and day 4 (3 samples).

ORGANISM(S): Homo sapiens

SUBMITTER: Andrew Hinton

PROVIDER: E-GEOD-16678 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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A distinct microRNA signature for definitive endoderm derived from human embryonic stem cells.

Hinton Andrew A Afrikanova Ivka I Wilson Mike M King Charles C CC Maurer Brian B Yeo Gene W GW Hayek Alberto A Pasquinelli Amy E AE

Stem cells and development 20100601 6

Human embryonic stem cells (hESCs) have the potential to differentiate into many adult cell types, and they are being explored as a resource for cell replacement therapies for multiple diseases. In order to optimize in vitro differentiation protocols, it will be necessary to elucidate regulatory mechanisms that contribute to lineage specification. MicroRNAs (miRNAs) are emerging as key regulators of hESC differentiation and embryonic development. In this study, we compare miRNA expression profil ...[more]

PMID: 19807270

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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

MicroRNA expression data from differentiation of human Cyt49 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 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 (Cyt49) 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-16687 | biostudies-arrayexpress

A distinct microRNA signature for definitive endoderm derived from human embryonic stem cells

Project description:This SuperSeries is composed of the following subset Series: GSE16678: MicroRNA expression data from differentiation of human Cyt49 ESCs into definitive endoderm in feeder-free conditions GSE16681: mRNA expression data from differentiation of human ESCs into definitive endoderm, Cyt49 on matrigel GSE16687: MicroRNA expression data from differentiation of human Cyt49 ESCs into definitive endoderm on MEF feeder layers GSE16689: MicroRNA expression data from differentiation of human H9 ESCs into definitive endoderm on MEF feeder layers Refer to individual Series

2010-07-30 | E-GEOD-16690 | biostudies-arrayexpress

mRNA expression data from differentiation of human ESCs into definitive endoderm, Cyt49 on matrigel

Project description: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 derived tissues: pancreas, liver, gut, lung. We used microarrays to detail the changes in mRNA expression during the transition from pluripotent hESCs into definitive endoderm. hESCs (Cyt49) were differentiated in the presence of Activin A and Wnt3A under low serum conditions to induce DE formation. Samples were collected at day 0, day 2 and day 4.

2010-07-30 | E-GEOD-16681 | biostudies-arrayexpress

Generation of organized anterior foregut epithelia from pluripotent stem cells using small molecules

Project description:Anterior foregut endoderm (AFE) gives rise to many tissue types of interest for therapeutic research including the esophagus, salivary glands, lung, thymus, parathyroid and thyroid. Despite its importance, only few reports describe the generation of AFE from pluripotent stem cells (PSCs) by directed differentiation. Here, we describe a novel protocol to derive a subdomain of AFE, identified by expression of Pax9, from PSCs using small molecules and chemically defined conditions. Generation of a reporter PSC line allows isolation and characterization of Pax9+ AFE cells. When transplanted in vivo, Pax9+ AFE can form several distinct types of complex anterior foregut epithelia including mucosal glands and stratified squamous epithelium. Finally, we show that the directed differentiation protocol can be used to generate AFE from DiGeorge Syndrome patient-specific human induced PSCs, thus creating a platform to produce anterior foregut derivatives for therapy and to enable the study of disorders of the AFE. Total RNA obtained from FACS purified from in vitro dervied mouse definitive endoderm, anterior foregut and ES cells. AFE cells were derived from a 129X1/SvJ background, DE cells from 129X1/SvJ x 129S1/SV-+p+Tyr- cKitlSl-J/+ (R1 ES cells) and non reporter ES cells from a 129P2/OlaHsd background.

2013-04-15 | E-GEOD-42139 | biostudies-arrayexpress

scRNA-seq to investigate endoderm differentiation from induced human pluripotent stem cells

Project description:Single-cell RNA-seq (scRNA-seq) on nocodazole and DMSO treated cells before and after differentiation into endoderm. hPSC colonies were treated with DMSO or 100ng/ml nocodazole for 16 hours and induced to differentiate into definitive endoderm for three days. Single cells were subsequently collected in either undifferentiated conditions (Und) or after 3 days of endoderm differentiation (Endoderm) and then sorted onto 384 well plates for Smart-Seq2 processing.

2019-02-09 | E-MTAB-7008 | biostudies-arrayexpress

RNA-seq of definitive endoderm differentiation of human embryonic stem cells in early G1 phase of the cell cycle

Project description:The experiment was designed to investigate transcriptional dynamics during definitive endoderm differentiation of human embryonic stem cells (hESCs) in early G1 phase of the cell cycle. For this, the FUCCI system was used to sort hESCs in Early G1 (EG1). Samples were taken at 0h (hESCs), 12h, 24h, 36h, 48h, 60h and 72h in triplicates. Total RNA was extracted using the GenElute Mammalian Total RNA Miniprep Kit (Sigma-Aldrich) and residual genomic DNA was removed using the On-Column DNase I Digestion Set (Sigma-Aldrich) following manufacturer’s instructions. The libraries were generated at a library fragment size between 100 bp to 1 kb with Stranded RNAseq Standard with Oligo dT pulldown. All samples were amplified with a standard 10 PCR cycle before sequencing. The samples were multiplexed and analysed by Illumina Hiseq V4 with a paired end read-length PE75. RNA-seq data analysis was performed following recommendations described in Conesa et al. (DOI https://doi.org/10.1186/s13059-016-0881-8).

2020-09-07 | E-MTAB-9194 | biostudies-arrayexpress

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

SMAD2/3 interactome in human pluripotent stem cells

Project description:This experiment was designed to determine the interactome of SMAD2/3 in human pluripotent stem cells (hPSCs). hPSCs were cultured in standard pluripotency-promoting conditions, or induced to differentiate towards the definitive endoderm lineage for 36h. Endogenous SMAD2/3 was immunoprecipitated from nuclear extracts in these two conditions using a specific antibody. Non-immune IgG immunoprecipitations were performed as negative controls. Three biological replicates per conditions were analyzed by quantitative label-free mass spectrometry.

2018-01-04 | PXD005285 | Pride

3' RNA-Seq (3'SEQ) analysis gene expression profiling at G1-S transition in human embryonic stem cells (hESCs) and hESC-derived endoderm cells

Project description:In this report, we examine transcripts on a genome-wide level between the synchronized cell cycles of hESCs and hESC-derived endoderm cells. We found 10347, 10299 and 10362 genes expressed in the G1, G1/S, and S phase of hESCs, respectively; 10333, 10227 and 10215 genes expressed at the G1, G1/S and S phase of derived endoderm. We compared the transcriptome between these data sets and identified genes with differentiated phase expression between hESCs and hESC-derived endoderm cells. Examination of the transcriptome at the G1-S transition in hESCs compared to hESC-derived endoderm cells.

2014-05-14 | E-GEOD-47117 | biostudies-arrayexpress

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