Mus musculus
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ABSTRACT:
PROVIDER: PRJNA121477 | ENA |
REPOSITORIES: ENA
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Project description:Exon-level transcriptome analysis of embryonal carcinoma (EC) and embryonic stem (ES) cell lines. To circumvent difficulties of isolating pure populations of cancer stem cells for the purpose of identifying malignancy-specific gene expression, we have compared exon-resolution transcriptomic profiles of five embryonal carcinoma (EC) cell lines, a histological subtype of germ cell tumour, to their non-malignant caricature, specifically six human embryonic stem (ES) cell lines. Both cell types are readily accessible, and were purified for undifferentiated cells only. We identified a set of 28 differentially expressed genes, many of which had cancer and stemness roles. Overexpression of the recently discovered pluripotency gene NR5A2 in malignant EC cells revealed an intriguing indication of how WNT-mediated dysregulation of pluripotency is involved with malignancy. At the exon-level, alternative splicing events were detected in ZNF195, DNMT3B and PMF1, and alternative promoters were detected for ASH2L and ETV5. These events were validated by RT-PCR-based methods in EC and ES lines, and further explored within a series of 25 primary tumours, where the alternative splicing event in the de novo DNA methyltransferase DNMT3B may have functional consequences. In conclusion, we have identified malignancy-specific gene expression differences within a rigorous pluripotent stem cell context. These findings are of particular interest for both germ cell tumour and ES cell biology, and in general to the concept of cancer stem cells. 5 EC and 6 ES cell lines gown on plastic and feeders respectively were sorted for the pluripotency marker SSEA3, then profiled on the Affymetrix Human Exon 1.0 ST platform. 3 additional EC lines grown on feeders and ES medium were also profiled in the same way. Data was analyzed using Qlucore (PCA), XRAY and limma (gene- and exon-level expression differences) and SAM (two-class pair-wise Significance of Microarrays).
2015-01-01 | E-GEOD-34855 | biostudies-arrayexpress
Project description:Gene-expression profile of human embryonic germ cells (EGCs), primordial germ cells (PGCs), embryonal carcinoma cells (ECCs), pluripotent embryonic stem cells (ESCs) and induced pluripotent stem cells (IPSCs)
2018-06-28 | E-MTAB-6851 | biostudies-arrayexpress
Project description:The Effect of Cell Aggregation on Gene Expression of Pluripotent Embryonal Carcinoma Cells
| PRJNA95237 | ENA
Project description:Gene expression profiles of undifferentiated mouse embryonal carcinoma cell strains (P19, P19CL6, and 4 P19CL6 sublines) were obtained, using Affymetrix GeneChip Mouse Genome 430A and 430B. Heart diseases such as cardiac infarction damage cardiomyocytes and consequently lead to significant loss of the contractile capacity of the heart. To repair functions of the injured heart, a great deal of research has attempted to develop regenerative medicine using pluripotent stem cell-based cardiomyocytes as cell therapy products. However, the efficiency of the current methods available for the cardiac differentiation of stem cells is insufficient for clinical settings. A comprehensive understanding of the mechanism involved in the cardiac differentiation of stem cells is necessary to improve the differentiation efficiency. To identify genes assosiated with cardiomyogenic potential, we isolated P19CL6 cell sublines possessing distinct properties in cardiomyogenesis and comprared their transcriptome profiles with those of mouse embryonal carcinoma P19 and P19CL6 cells. Total RNA isolated from undifferentiated EC cell strains (P19 cells, P19CL6 cells, and 4 P19CL6 sublines) using Affymetrix chips MOE430A and MOE430AB. CEL files unavailable.
2011-01-26 | E-GEOD-26875 | biostudies-arrayexpress
Project description:Exon-level transcriptome analysis of embryonal carcinoma (EC) and embryonic stem (ES) cell lines. To circumvent difficulties of isolating pure populations of cancer stem cells for the purpose of identifying malignancy-specific gene expression, we have compared exon-resolution transcriptomic profiles of five embryonal carcinoma (EC) cell lines, a histological subtype of germ cell tumour, to their non-malignant caricature, specifically six human embryonic stem (ES) cell lines. Both cell types are readily accessible, and were purified for undifferentiated cells only. We identified a set of 28 differentially expressed genes, many of which had cancer and stemness roles. Overexpression of the recently discovered pluripotency gene NR5A2 in malignant EC cells revealed an intriguing indication of how WNT-mediated dysregulation of pluripotency is involved with malignancy. At the exon-level, alternative splicing events were detected in ZNF195, DNMT3B and PMF1, and alternative promoters were detected for ASH2L and ETV5. These events were validated by RT-PCR-based methods in EC and ES lines, and further explored within a series of 25 primary tumours, where the alternative splicing event in the de novo DNA methyltransferase DNMT3B may have functional consequences. In conclusion, we have identified malignancy-specific gene expression differences within a rigorous pluripotent stem cell context. These findings are of particular interest for both germ cell tumour and ES cell biology, and in general to the concept of cancer stem cells.
2015-01-01 | GSE34855 | GEO
Project description:Xenografts of human pluripotent stem cells and embryonal carcinoma cells
| PRJNA376568 | ENA
Project description:Pluripotent stem cell lines derived from embryos of different stages have distinct pluripotent ground states, but similar levels of the transcription factor Oct4. Epiblast-derived pluripotent stem cells (EpiSCs), in contrast to embryonic stem (ES) cells, cannot form chimeras. We show that EpiSCs express lower levels of the transcription factors Sox2 and Klf4 than ES cells and have limited reprogramming potential, as shown by cell fusion. Sox2 overexpression dramatically increases the reprogramming potential, chimera formation, and germline contribution of EpiSCs. Therefore, although Oct4 is essential for reprogramming, the level of Sox2 defines both the reprogramming capability and the pluripotent ground states. RNA samples to be analyzed on microarrays were prepared using Qiagen RNeasy columns with on-column DNA digestion. 300 ng of total RNA per sample was used as input into a linear amplification protocol (Ambion), which involved synthesis of T7-linked double-stranded cDNA and 12 hrs of in-vitro transcription incorporating biotin-labelled nucleotides. Purified and labelled cRNA was then hybridized for 18 hrs onto MouseRef-8 v2 expression BeadChips (Illumina) according to the manufacturer's instructions. After washing, as recommended, chips were stained with streptavidin-Cy3 (GE Healthcare) and scanned using the iScan reader (Illumina) and accompanying software. Samples were hybridized as biological replicates. 12 sample types were analyzed, each of them in duplicate. ESCm: Mouse ESC male; ESCf: Mouse ESC OG2 female; F9 EC: F9 EC (mouse embryonic carcinoma cell); F9-Sox2: F9 EC (mouse embryonic carcinoma cell) overexpressing wild type Sox2; EpiSCf: Mouse EpiSC OG2 female; Epi-Sox2f: Mouse EpiSC Sox2 (OG2 female) overexpressing wild type Sox2; P19 EC: P19 EC (mouse embryonic carcinoma cell); P19-Sox2: P19 EC (mouse embryonic carcinoma cell) overexpressing wild type Sox2; EpiSCm: Mouse EpiSC (GOF18 male) (duplicates); EpiSox2mL2: Mouse EpiSC Sox2 (GOF18 male) overexpressing wild type Sox2 cultured in condition EpiSC medium (CM); EpiSox2mE1: Mouse EpiSC Sox2 (GOF18 male) overexpressing wild type Sox2 cultured in ESC medium (ESC like1); EpiSox2mE2: Mouse EpiSC Sox2 (GOF18 male) overexpressing wild type Sox2 cultured in ESC medium (ESC like2).
2010-12-31 | E-GEOD-15358 | biostudies-arrayexpress
Project description:Here we analyzed undifferentiated cells and perfomed the Teratoma assay for a normal human embryonic stem cell line (H9(+Dox)), a human embryonic stem cell line with a mesendodermal differentiation bias (H9Hyb), a normal human induced pluripotent stem cell line (LU07), a human induced pluripotent stem cell line with reactivated transgenes (LU07+Dox) and a human embryonal carcinoma cell line (EC). The ability to form teratomas in vivo containing multiple somatic cell types is regarded as functional evidence of pluripotency for human pluripotent stem cells (hPSCs). Since the Teratoma assay is animal-dependent, laborious and only qualitative, the PluriTest and the hPSC ScoreCard assay have been developed as in vitro alternatives. Here we compared normal hPSCs, induced hPSCs (hiPSCs) with reactivated reprogramming transgenes and human embryonal carcinoma (hEC) cells in these assays. While normal hPSCs gave rise to typical teratomas, the xenografts of the hEC cells and the hiPSCs with reactivated reprogramming transgenes were largely undifferentiated and malignant. The hPSC ScoreCard assay confirmed the line-specific differentiation propensities in vitro. However, when undifferentiated cells were analysed with PluriTest only hEC cells were identified as abnormal whereas all other cell lines were indistinguishable and resembled normal hPSCs. Our results indicate that pluripotency assays are best selected on the basis of intended downstream applications.
2017-02-24 | GSE95284 | GEO
Project description:Here we perfomed the Teratoma assay for a normal human embryonic stem cell line (H9(+Dox)), a human embryonic stem cell line with a mesendodermal differentiation bias (H9Hyb), a normal human induced pluripotent stem cell line (LU07), a human induced pluripotent stem cell line with reactivated transgenes (LU07+Dox) and a human embryonal carcinoma cell line (EC) and anayzed their gene expression. The ability to form teratomas in vivo containing multiple somatic cell types is regarded as functional evidence of pluripotency for human pluripotent stem cells (hPSCs). Since the Teratoma assay is animal-dependent, laborious and only qualitative, the PluriTest and the hPSC ScoreCard assay have been developed as in vitro alternatives. Here we compared normal hPSCs, induced hPSCs (hiPSCs) with reactivated reprogramming transgenes and human embryonal carcinoma (hEC) cells in these assays. While normal hPSCs gave rise to typical teratomas, the xenografts of the hEC cells and the hiPSCs with reactivated reprogramming transgenes were largely undifferentiated and malignant. The hPSC ScoreCard assay confirmed the line-specific differentiation propensities in vitro. However, when undifferentiated cells were analysed with PluriTest only hEC cells were identified as abnormal whereas all other cell lines were indistinguishable and resembled normal hPSCs. Our results indicate that pluripotency assays are best selected on the basis of intended downstream applications.
2017-02-24 | GSE95285 | GEO
Project description:Phf19 knockdown effect on F9 embryonal carcinoma cells
| PRJNA182015 | ENA