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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcription profile of primordium gut organs

ABSTRACT: Induced pluripotent stem (iPS) cells are a novel stem cell population induced from mouse and human adult somatic cells through reprogramming by transduction of defined transcription factors. Recently, researchers success in generation various cells from iPSCs. Lung progenitor cells are able to differentiate to all of the cells exist in adult lung, attract attention for regenerative medicine. It is known to present between embryonic day 9.5 from 13.5 in mice. We can realized at regenerative medicine in lung using lung progenitor cell surface markers defined by compering each endoderm primordia of organ formation. We investigated the differences in gene expression of each endoderm organ. Mouse gut organs morphogenesis begin at E9.5-E11.5. The primordium lung, esophagus, stomach, and intestine at E11.5 were dissected and analysed transcription profile.

ORGANISM(S): Mus musculus

SUBMITTER: Mari Sekine

PROVIDER: E-GEOD-55312 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Transcription profile of primordium gut organs

Project description:The mechanisms of gastrointestinal morphogenesis in mammals are not well understood. This is partly due to the lack of organ specific gene expression pattern in the gastrointestinal tract during development. The initiation of organ bud formation occurs at E9.5-E11.5 in mice. These primordia for the digestive organs, including esophagus, stomach, and intestine, protrude from a tube-like structured endoderm, and have their own distinct morphogenesis. Thus, using mouse embryos, we surveyed transcription of prospective these three regions at E11.5 during gastrointestinal morphogenesis. This early digestive organ specific transcription profile will be useful for understanding of the mechanisms of gastrointestinal development. Mouse gut organs morphogenesis begin at E9.5-E11.5. The primordium esophagus, stomach, and intestine at E11.5 were dissected and analysed transcription profile.

2012-05-31 | E-GEOD-30742 | biostudies-arrayexpress

Transcription profile of primordium gut organs

Project description:Induced pluripotent stem (iPS) cells are a novel stem cell population induced from mouse and human adult somatic cells through reprogramming by transduction of defined transcription factors. Recently, researchers success in generation various cells from iPSCs. Lung progenitor cells are able to differentiate to all of the cells exist in adult lung, attract attention for regenerative medicine. It is known to present between embryonic day 9.5 from 13.5 in mice. We can realized at regenerative medicine in lung using lung progenitor cell surface markers defined by compering each endoderm primordia of organ formation. We investigated the differences in gene expression of each endoderm organ.

2014-03-25 | GSE55312 | GEO

Generation of induced pluripotent stem cells in rabbits: potential experimental models for human regenerative medicine

Project description:Human induced pluripotent stem (iPS) cells have the potential to establish a new field of promising regenerative medicine. Therefore, the safety and the efficiency of iPS-derived cells must be tested rigorously using appropriate animal models before human trials can commence. Here, we report the establishment of rabbit iPS cells as the first human-type iPS cells generated from a small laboratory animal species. Using lentiviral vectors, four human reprogramming genes (c-MYC, KLF4, SOX2 and OCT3/4) were introduced successfully into adult rabbit liver and stomach cells. The resulting rabbit iPS cells closely resembled human iPS cells; they formed flattened colonies with sharp edges and proliferated indefinitely in the presence of bFGF. They expressed the endogenous pluripotency markers c-MYC, KLF4, SOX2, OCT3/4 and NANOG, while the introduced human genes were completely silenced. Using in vitro differentiating conditions, rabbit iPS cells readily differentiated into ectoderm, mesoderm and endoderm. They also formed teratomas containing a variety of tissues of all three germ layers in immunodeficient mice. Thus, the rabbit iPS cells fulfilled all of the requirements for the acquisition of the fully reprogrammed state, showing high similarity to their embryonic stem (ES) cell counterparts we generated recently. However, their global gene expression analysis revealed a slight, but rigid difference between these two types of rabbit pluripotent stem cells. The rabbit model should enable us to compare iPS cells and ES cells under the same standardized conditions in evaluating their ultimate feasibility for pluripotent cell-based regenerative medicine in humans. Comparison of rabbit embryonic stem cells, rabbit somatic cells, and rabbit induced pluripotent stem cells at several timing (passage number 6, 7, 22, 23) of cultures. Eight samples were used for assessment.

2010-07-28 | E-GEOD-23190 | biostudies-arrayexpress

Functional Roles of Hdac1/2 in lung development

Project description:Hdac1/2 are important epigenetic factors, yet their functional roles in specific tissues inluding lung is not determined. We used the conditional knockout model of Hdac1/2 to determine their roles in lung development. To explore the genes that are regulated by Hdac1/2 during lung development, we performed microarray analysis of Shhcre control and Hdac1/2DKO lungs at E11.5 embryos.

2013-12-31 | E-GEOD-39946 | biostudies-arrayexpress

Data in support of the equine mesenchymal stem cell surface proteome for mining for new surface markers

Project description:Regenerative medicine in aims to restore structure and function to tissues or organs damaged by time, disease or injury. Stem cells have great potential for tissue repair and regeneration, why they are intensely investigated in equine clinical research. However, before any type of stem cell can be applied in practice, it is crucial that the isolated stem cells have been definitively characterised by a set of specific functional or phenotypic markers. This project includes a surface mapping of equine mesenchymal (MSC) stem cell surface proteome.

2018-11-04 | PXD008884 | Pride

Transcription profile of adipose derived mesenchymal stem cells separated by cell surface protein N-cadherin.

Project description:Mesenchymal stem cells (MSCs) are one of most promising stem cell sources for regenerative medicine. MSCs have a differention ability into several tissues. However, their differentiation efficiency is considered quite limited. Especially, the differentiation efficiency into cardiomyocytes is very low. N-cadherin is one of the cell surface protein that is expressed in developing and adult cardiomyocytes. We found that cell surface expression of N-cadherin in MSCs shows good correlation with the cardiomyogenic differentiation ability. We also analyzed the expression profiles of N-cadherin-positive and N-cadherin-negative fraction by microarray. We found that N-cadherin-positive MSCs show higher expression of some of the cardiomyogenesis-related genes than N-cadherin-negative MSCs. The ASCs were maintained in MesenPRO RSTM Medium. The ASCs were harvested in a cell dissociation buffer. The ASCs were incubated with biotinylated anti N-cadherin antibody and next incubated with streptavidin M-bM-^@M-^SAPC. Subsequently cells were incubated with anti-APC microbeads. Immunomagnetic separation of N-cadherin+ cells were performed with autoMACSTMPro separator applying the separation program M-bM-^@M-^Xdepl025M-bM-^@M-^Y

2013-10-29 | E-GEOD-35232 | biostudies-arrayexpress

Dynamic developmental signaling logic underlying lineage bifurcations during human endoderm induction and patterning from pluripotent stem cells [Endoderm RNA-seq and ChIP-seq data sets]

Project description:Unraveling complex signaling programs animating developmental lineage-decisions is pivotal to differentiate human pluripotent stem cells (hPSC) into pure populations of desired lineages for regenerative medicine. Developmental signals are strikingly temporally dynamic: BMP and Wnt initially specify primitive streak (progenitor to endoderm) yet 24 hours later suppress endoderm and induce mesoderm. At lineage bifurcations we show mutually-exclusive embryonic lineages are segregated through cross-repressive signals: TGFM-NM-2 and BMP/MAPK duel to respectively specify pancreas versus liver from endoderm. Unilateral endodermal differentiation requires blockade of alternative fates at every stage, revealing a universal developmental strategy for efficient differentiation and anterior-posterior patterning of diverse hPSC lines into highly-pure endodermal populations. This culminated in hPSC-derived hepatic progenitors that, for the first time, engraft long-term in genetically-unconditioned mouse livers and secrete human albumin. Finally, thirty transcriptional and chromatin state maps capturing endoderm commitment revealed endodermal enhancers reside in an unanticipated diversity of "pre-enhancer" chromatin states before activation. Endoderm RNA-seq and ChIP-seq data sets

2013-11-22 | E-GEOD-52657 | biostudies-arrayexpress

Gene expression profiling of Six2-positive nephron progenitors from mouse embryo

Project description:Nephron progenitors in the embryonic kidney propagate while generating differentiated nephrons. However, the progenitors in mice terminally differentiate shortly after birth. We defined culture conditions to selectively propagated nephron progenitors in vitro in an undifferentiated state. To understand how expression profiles of Six2+ cells changed during culture in vitro compared with in vivo, we performed microarray analysis of Six2+ cells at E11.5 (starting material) and P0 (experiencing 8 days in vivo), and cultured Six2+ cells at E11.5 for 8 days or 19 days. Microarray analysis were performed with isolated Six2-positive nephron progenitors from transgenic mice embryo at E11.5 or P0, and cultured E11.5 Six2+ cells for 8 or 19 days in conditioned media. P0 non-progenitors represent Six2-GFP-negative cells at P0.

2016-04-14 | E-GEOD-79024 | biostudies-arrayexpress

E11.5 Mouse Endodermal Organ Gene Expression

Project description:To study gene expression during endodermal organogenesis, we sought to identify genes expressed in restricted domains during organogenesis. For gene expression analysis, six morphologically distinct endodermal domains were dissected at E11.5: the esophageal region; the lung and distal tracheal region; the stomach region; the hepatic region; the dorsal and ventral pancreatic region; and the intestinal region. Through flow cytometric separation using EpCAM expression to distinguish endoderm from surrounding mesenchyme, pure populations of endoderm progenitors from the esophageal, lung, stomach, pancreatic, and intestinal regions were isolated. Expression of Liv2 was used to isolate a pure population of hepatic endoderm progenitors. Keywords: cell type comparison

2008-12-30 | GSE13040 | GEO

Transcription profiling of mouse strain differences in e11.5 XY gonad transcriptome suggest a mechanism for the sensitivity of C57BL/6J to sex reversal

Project description:Transcriptional profiling of individual mouse embryonic (e11.5) XY gonads comparing inbred strains that are sensitive (C57BL/6J) and resistant (129S1/SvImJ) to XY sex reversal, and their reciprocal F1 hybrids. Experiment Overall Design: Two-color Agilent microarray profiles of 20 individual pairs of e11.5 XY gonads, including 5- C57BL/6J, 5- 129S1/SvImJ, 5- (B6x129S1)F1, and 5- (129S1xB6)F1 samples. Within each strain, samples were collected from multiple litters to account for potential litter biases. All samples were processed following the same protocol.

2009-12-03 | E-GEOD-16917 | biostudies-arrayexpress

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