The European Bank for Induced Pluripotent stem cells (EBiSC) is designed to address the increasing demand by iPSC researchers for quality-controlled, disease-relevant research grade iPSC lines, data and cell services.In this study Whole Genome Sequencing was performed on a selection of lines from the project.
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PROVIDER: EGAS00001002755 | EGA |
REPOSITORIES: EGA
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Project description:In comprehensive glycome analysis with a high-density lectin microarray, we have previously shown that the recombinant N-terminal domain of the lectin BC2L-C from Burkholderia cenocepacia (rBC2LCN) binds exclusively to undifferentiated human induced pluripotent stem (iPS) cells and embryonic stem (ES) cells but not to differentiated somatic cells. Here we demonstrate that podocalyxin, a heavily glycosylated type1 transmembrane protein, is the predominant glycoprotein ligand of rBC2LCN on human iPS cells and ES cells. When analyzed by DNA microarray, podocalyxin was found to be highly expressed in both iPS cells and ES cells. Western and lectin blotting revealed that rBC2LCN binds predominantly to podocalyxin with a high molecular weight of more than 240 kDa in undifferentiated iPS cells of six different origins and four ES cell lines, but no binding was observed in either differentiated mouse feeder cells or somatic cells. The specific binding of rBC2LCN to podocalyxin prepared from a large set of iPS cells (138 types) and ES cells (15 types) was also confirmed using a high-throughput antibody-overlay lectin microarray. Alkaline digestion greatly reduced the binding of rBC2LCN to podocalyxin, indicating that the major glycan ligands of rBC2LCN are presented on O-glycans. Furthermore, rBC2LCN was found to exhibit significant affinity to a branched Oglycan comprising an H type3 structure as the most probable rBC2LCN glycan ligand (Kd, 4.0 x 10-5 M) prepared from human 201B7 iPS cells, suggesting that H type3 is a novel potential pluripotency marker. We conclude that podocalyxin is the predominant glycoprotein ligand of rBC2LCN on human iPS cells and ES cells. Gene expressions in human embryonic stem cells (ESCs) and human induced pluripotent stem cells (iPSCs). Human iPS cells (MRC5-iPS, AM-iPS, UtE-iPS, PAE-iPS) were induced from four different somatic cells by infection of the retroviral vectors pMXs encoding OCT3/4, SOX2, KLF4 and c-MYC, simultaneously. Human iPS cells (TIG/MKOS#19, #56, #106) were generated through reprogramming by Sendai virus infection-mediated expression of OCT4, SOX2, KLF4, and c-MYC.
2015-10-28 | E-GEOD-42099 | biostudies-arrayexpress
Project description:In comprehensive glycome analysis with a high-density lectin microarray, we have previously shown that the recombinant N-terminal domain of the lectin BC2L-C from Burkholderia cenocepacia (rBC2LCN) binds exclusively to undifferentiated human induced pluripotent stem (iPS) cells and embryonic stem (ES) cells but not to differentiated somatic cells. Here we demonstrate that podocalyxin, a heavily glycosylated type1 transmembrane protein, is the predominant glycoprotein ligand of rBC2LCN on human iPS cells and ES cells. When analyzed by DNA microarray, podocalyxin was found to be highly expressed in both iPS cells and ES cells. Western and lectin blotting revealed that rBC2LCN binds predominantly to podocalyxin with a high molecular weight of more than 240 kDa in undifferentiated iPS cells of six different origins and four ES cell lines, but no binding was observed in either differentiated mouse feeder cells or somatic cells. The specific binding of rBC2LCN to podocalyxin prepared from a large set of iPS cells (138 types) and ES cells (15 types) was also confirmed using a high-throughput antibody-overlay lectin microarray. Alkaline digestion greatly reduced the binding of rBC2LCN to podocalyxin, indicating that the major glycan ligands of rBC2LCN are presented on O-glycans. Furthermore, rBC2LCN was found to exhibit significant affinity to a branched Oglycan comprising an H type3 structure as the most probable rBC2LCN glycan ligand (Kd, 4.0 x 10-5 M) prepared from human 201B7 iPS cells, suggesting that H type3 is a novel potential pluripotency marker. We conclude that podocalyxin is the predominant glycoprotein ligand of rBC2LCN on human iPS cells and ES cells.
2015-10-28 | GSE42099 | GEO
Project description:The ectopic expression of a defined set of transcription factors, Oct4, Klf4, Sox2, and c-Myc, reprograms mouse embryonic fibroblasts (MEFs) and adult tail-tip fibroblasts (TTFs) into embryonic stem (ES)-like cells called induced pluripotent stem (iPS) cells. iPS cells have been generated from a variety of somatic cells, including embryonic and adult dermal fibroblasts, epithelial cells of the liver and stomach, pancreatic b cells, mature B lymphocytes, and adult neural stem cells (NSCs). While these studies demonstrated that most somatic cells are capable of acquiring pluripotency with minimal gene transduction, the poor efficiency of cell reprogramming and the uneven quality of iPS cells are still important problems. In particular, the choice of cell type most suitable for inducing high-quality iPS cells remains unclear. Here, we generated iPS cells from PDGFRa+ Sca-1+ (PaS) cells that represent highly enriched adult mouse mesenchymal stem cells (MSCs) and PDGFRa- Sca-1- osteo-progenitor (OP) cells. When we compared the induction efficiency and quality of individual iPS clones, MSCs had a higher reprogramming efficiency compared with OP cells and TTFs. The iPS cells induced from MSCs by Oct3/4, Sox2, and Klf4 appeared to be the closest equivalent to ES cells by DNA microarray gene profile and germline-transmission efficiency. We conclude that prospectively isolated MSCs are a promising candidate for the efficient and stable generation of high-quality iPS cells.
2010-08-21 | GSE23717 | GEO
Project description:The IMBA stem cell bank, iPSC Biobank, is a collection of induced pluripotent stem cell lines (iPSC lines) produced from skin and blood cells. The iPSC Biobank is integrated into the IMBA Stem Cell Core Facility. It stores and provides high-quality reference control panels of iPSC clones as a tool to the research community. The resource is available to all scientists and commercial institutions. The ethical guidelines of the iPSC Biobank are always based on prevailing laws and internal regulations.
| EGAS00001006262 | EGA
Project description:Induced pluripotent stem cells (iPSCs) are commonly generated by transduction of Oct4, Sox2, Klf4 and Myc (OSKM) into somatic cells. Though iPSCs are pluripotent, they frequently exhibit high variation in their quality as measured by chimera contribution and tetraploid (4n) complementation. Thus, improving the quality of iPSCs is an indispensable prerequisite for future iPSC-based therapy. Here we show that one major determinant for iPSCs quality is the selection of the reprogramming factors combination. Ectopic expression of Sall4, Nanog, Esrrb and Lin28 (SNEL) in MEFs efficiently generated high quality iPSCs as compared to other combinations of factors. SNEL-iPSCs produced approximately 5 times more efficiently “all-iPSC” mice compared to OSKM-iPSCs. While differentially methylated regions, transcript number of master regulators, establishment of ESC-specific super enhancers, and global aneuploidy were comparable between the lines, aberrant expression of 1,765 genes, trisomy of chromosome 8 and abnormal H2A.X deposition were frequently observed in poor quality OSKM-iPSCs. For high-quality iPSCs, H2A.X pattern of SNEL is most similar to that of ESC, OSK and OSKM have more devoid regions than SNEL iPSCs. Compare H2A.X deposition pattern of the OSKM 4-factor iPS cell lines (4N-), SNEL 4-factor iPS cell lines (4N+) with ChIP-Seq. The same background ES cell line as the control line.
2014-09-07 | E-GEOD-55731 | biostudies-arrayexpress
Project description:ATAC-seq samples from 2 species and 2 cell types were generated to study cis-regulatory element evolution. Briefly, previously generated urinary stem cell derived iPS-cells (Homo sapiens) of 2 human individuals and fibroblast derived cynomolgus macaque iPSCs (Macaca fascicularis) of 2 individuals (Geuder et al. 2021) were differentiated to neural progenitor cells via dual-SMAD inhibition as three-dimensional aggregation culture (Chambers et al. 2009; Ohnuki et al. 2014). The NPC lines were cultured in NPC proliferation medium and passaged 2 - 4 times until they were dissociated and subjected to ATAC-seq together with the respective iPSC clones. ATAC-seq libraries were generated using the Omni-ATAC protocol (Corces et al. 2017) with minor modifications.
2023-10-25 | E-MTAB-13373 | biostudies-arrayexpress
Project description:There are no described quality assurance mechanisms for newly formed stem cells. We observed intimate interactions between macrophages and blood stem cells in zebrafish embryos. Stressed stem cells were marked by surface Calreticulin, which stimulates macrophage interaction as an eat me signal. Macrophage-stem cell interactions either lead to removal of cytoplasmic material and stem cell proliferation or resulted in complete stem cell engulfment. Calreticulin knock down or embryonic macrophage depletion reduced the number of stem cell clones into adulthood. Our work supports a model in which embryonic macrophages determine hematopoietic clonality by monitoring stem cell quality.
2022-02-04 | MSV000088780 | MassIVE
Project description:The present study aimed at studying the rainbow trout egg transcriptome using 9152-cDNA microarrays after natural or controlled ovulation. The analysis of egg transcriptome after natural or controlled ovulation led to the identification of 26 genes. We observed that both hormonal induction and photoperiod control of ovulation induced significant changes in the egg mRNA abundance of specific genes. We demonstrate that hormonal induction of ovulation has an impact on the egg mRNA abundance of specific genes even though the resulting effects on the developmental potential of the egg is so far unknown. In addition, we also identified 1 gene exhibiting a differential mRNA abundance in eggs of varying developmental potential. Keywords: Egg quality-dependent
2006-10-03 | GSE5928 | GEO
Project description:During development, nephron progenitor forming one million nephrons, a functional unit in the kidney. However, nephron progenitor ceases before birth in human when they terminally differentiated to the nephron. Our lab established the method for induction of nephron progenitors from mouse Embryonic Stem (ES) cells and/or human induced Pluripotent Stem Cells (iPSCs) (Taguchi et al., Cell Stem Cell. 2014, 2017). For application of induced nephron progenitors to regenerative medicine, a large number of cells are required such as disease modeling and drug screening. To selectively propagate human iPS-derived nephron progenitors in vitro in an undifferentiated state, we developed SIX2-GFP iPS line and optimized culture condition of induced nephron progenitors by modifying our previously developed condition (Tanigawa et al., Cell Rep. 2016). To understand how whole gene expression profiles of human iPS-derived nephron progenitor cells are changed during culture, we isolated nephron progenitor cells by FACS and cultured in our defined culture condition. Purified RNAs from cultured cells at day 7 or un-cultured nephron progenitor cells were analyzed by RNA-seq.
2019-08-01 | GSE118729 | GEO
Project description:Hematopoiesis generated from human embryonic stem cells (ES) and induced pluripotent stem cells (iPS) are unprecedented resources for cell therapy. We compared hematopoietic differentiation potentials from ES and iPS cell lines originated from various donors and derived them using integrative and non-integrative vectors. Significant differences in differentiation toward hematopoietic lineage were observed among ES and iPS. The ability of engraftment of iPS or ES-derived cells in NOG mice varied among the lines with low levels of chimerism. iPS generated from ES cell-derived mesenchymal stem cells (MSC) reproduce a similar hematopoietic outcome compared to their parental ES cell line. We were not able to identify any specific hematopoietic transcription factors that allow to distinguish between good versus poor hematopoiesis in undifferentiated ES or iPS cell lines. However, microarray analysis showed genes differentially expressed in ES and iPS cell lines according to their hematopoietic potential. These results demonstrate the influence of genetic background in variation of hematopoietic potential rather than the reprogramming process.
2015-11-17 | GSE75051 | GEO