Expression data from human induced Pluripotent Stem Cel (iPSC) and Embryoid Body (EB)
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA882068 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:We analyzed the comprehensive gene expression of human iPSC and EB. EB was induced for 7days.
2022-09-24 | GSE213687 | GEO
Project description:Expression profiling of a 16 day mouse embryoid body (EB) differentiation time course.
2008-06-01 | E-TABM-433 | biostudies-arrayexpress
Project description:Human pluripotent stem cells were differentiated by size-controlled embryoid body (EB) formation in defined neutral, ectoderm, endoderm and mesoderm conditions. EB's were analysed at 4, 10 and 16 days post induction by real-time PCR using the Fludigm Deltagene primers and probes.
2017-06-20 | GSE97963 | GEO
Project description:Human Primordial Germ Cell (PGC)-like cells (PGCLC) were specified in vitro from naive-like hiPS cell lines. To evaluate the first steps of PGCLC differentiation, we performed scRNA-seq (droplet-based technology, 10x) on cell suspension from embryoid body (EB) obtained after EB aggregation followed by 4 days of culture (EBd4) with cocktail of cytokines (BMP4, LIF, SCF, EGF and ROCK inhibitor) supplemented with 0.1 mM 2-mercaptoethanol and 15% KSR. In this study, two pools of embryoid bodies (EBD4_A, EBD4_B) were cultured independently for for further encapsulation and sequencing.
2022-11-29 | E-MTAB-12089 | biostudies-arrayexpress
Project description:Stem cell differentiation strategies and optimization for generating lineage-specific cells and tissues most frequently rely on a three-dimensional embryoid body (EB) intermediate. We previously applied nanotechnology tools of photolithography to generate custom microarrays that allow high throughput uniform formation of EBs of custom size for precise downstream analysis. Formation of EBs of 200 or 500 micron size revealed distinct morphological differences that are single or multicystic cores, respectively, independent of method of formation from single cells or two-dimensional (2D) clusters. Here we utilize photolithographic array generated EBs to obtain 3D cultures under a standardized platform for transcriptome analysis to compare EB size and the method of EB formation from single cells or mechanically passaged 2D clusters. Our analysis evaluates RNA expression in EBs formed from the human embryonic stem cell (hESC) line WA09 and from ethnically diverse human induced pluripotent stem cell lines (ED-iPSC) of African American and Hispanic Latino ethnicity recently derived in our laboratory. This is the first comprehensive study on EB transcriptomes including multiple size parameters, EB formation methodologies, and ethnicities. Our analysis indicates upregulation of genes involved in wound healing for mechanically passaged cells and of genes for embryonic tube formation in 500 micron multicystic EBs. We propose that EB maturation may be a longer process then previously realized. In addition, the type or extent of maturation possible may be influenced by EB size, with larger EBs capable of more extensive remodeling as revealed by multicystic morphology and initiation of early tube formation pathways while retaining pluripotency status. We anticipate that this information will be broadly useful to the stem cell and bioengineering communities in optimization of tissue engineering with pluripotent stem cells and understanding sources of variation. mRNA profiles by RNA-seq from embryoid bodies generated by different methods
2015-12-05 | E-GEOD-74792 | biostudies-arrayexpress
Project description:Snai1 is a master factor of epithelial to mesenchymal transitioin (EMT), however, its role in embryonic stem cell (ESC) differentiation and lineage commitment remains undefined. We used microarrays to compare the global programme of gene expression between control and Snai1 knockout ESCs-derived EB and teratoma. For EBs, control and Snai1 knockout ESCs were cultured as embryoid bodies in spotaneous differentiation media, RNA of 5 days EBs were collected for Affymetrix microarrays. For teratomas, control and Snai1 knockout ESCs were injected into nude mice to form teratomas. RNA of 6 weeks were collected for Affymetrix microarrays.
2013-12-10 | E-GEOD-53106 | biostudies-arrayexpress
Project description:To examine global gene expression changes during differentiation of epiblast stem cells (EpiSCs) induced by embryoid body (EB) formation, we performed RNA-seq analysis.
2018-06-01 | E-MTAB-5343 | biostudies-arrayexpress
Project description:Stem cell differentiation strategies and optimization for generating lineage-specific cells and tissues most frequently rely on a three-dimensional embryoid body (EB) intermediate. We previously applied nanotechnology tools of photolithography to generate custom microarrays that allow high throughput uniform formation of EBs of custom size for precise downstream analysis. Formation of EBs of 200 or 500 micron size revealed distinct morphological differences that are single or multicystic cores, respectively, independent of method of formation from single cells or two-dimensional (2D) clusters. Here we utilize photolithographic array generated EBs to obtain 3D cultures under a standardized platform for transcriptome analysis to compare EB size and the method of EB formation from single cells or mechanically passaged 2D clusters. Our analysis evaluates RNA expression in EBs formed from the human embryonic stem cell (hESC) line WA09 and from ethnically diverse human induced pluripotent stem cell lines (ED-iPSC) of African American and Hispanic Latino ethnicity recently derived in our laboratory. This is the first comprehensive study on EB transcriptomes including multiple size parameters, EB formation methodologies, and ethnicities. Our analysis indicates upregulation of genes involved in wound healing for mechanically passaged cells and of genes for embryonic tube formation in 500 micron multicystic EBs. We propose that EB maturation may be a longer process then previously realized. In addition, the type or extent of maturation possible may be influenced by EB size, with larger EBs capable of more extensive remodeling as revealed by multicystic morphology and initiation of early tube formation pathways while retaining pluripotency status. We anticipate that this information will be broadly useful to the stem cell and bioengineering communities in optimization of tissue engineering with pluripotent stem cells and understanding sources of variation.
2015-12-05 | GSE74792 | GEO
Project description:Embryonic stem (ES) cells, when grown in suspension culture without feeders, spontaneously form round structures known as embryoid bodies. Given the appropriate conditions, these cells can differentiate over time into precursors of all three germ layers. Embryoid bodies, in a disorganized way, mimic early embryonic development to a certain extent and can be used as a synchronously differentiating large scale source of tissue for the study of biological determinants of early differentiation. Embryoid bodies have been used as a source for most early protocols that derive specific differentiated cell types from undifferentiated ES cells, although some protocols, notably those that derive neurons from ES cells, have moved on from EBs as a result of varying replicability and yield. We have decided to look at the transcriptomic profiles of embryoid bodies during the initial stages of embryoid body formation and differentiation, in order to pinpoint novel determinants of key developmental stages. Keywords: time course
2007-08-15 | GSE8766 | GEO
Project description:This work indicates Hnrnpll depletion mES cells cannot exit from pluripotency programme, showing embryoid body formation deficiency and no spontaneous differentiation withdraw LIF. Hnrnpll promotes multiple ES cell preferred-exon skipping during ES cells differentiation, to reduce the ES cells specific isoform and facilitate ES cells exit from pluripotency towards differentiation.
2020-12-06 | GSE136955 | GEO