Genome wide profiling of human embryonic stem cells (hESCs), their derivatives and embryonal carcinoma cells to develop base profiles of U.S. Federal government approved hESC lines
| Autor: | Huai Li, Soojung Shin, Catherine M. Schwartz, Franz Josef Mueller, Ming Zhan, Haipeng Xue, Jeanne F. Loring, Steffen Oeser, David L. Barker, Mark P. Mattson, Xianmin Zeng, Ying Liu, Eugene Chudin, Shawn C. Baker, Timothy K. McDaniel, Mahendra S. Rao, Rodolfo Gonzalez |
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| Rok vydání: | 2006 |
| Předmět: |
Embryoid body
Computational biology Biology Genome Cell Line Massively parallel signature sequencing Embryonal carcinoma 03 medical and health sciences 0302 clinical medicine Carcinoma Embryonal medicine Humans lcsh:QH301-705.5 Oligonucleotide Array Sequence Analysis 030304 developmental biology 0303 health sciences Genome Human Gene Expression Profiling Stem Cells Embryo Mammalian medicine.disease Molecular biology Embryonic stem cell United States Gene expression profiling Embryo Research lcsh:Biology (General) 030220 oncology & carcinogenesis embryonic structures Government Regulation Human genome Stem cell Research Article Developmental Biology |
| Zdroj: | BMC Developmental Biology BMC Developmental Biology, Vol 6, Iss 1, p 20 (2006) |
| ISSN: | 1471-213X |
| DOI: | 10.1186/1471-213x-6-20 |
| Popis: | Background In order to compare the gene expression profiles of human embryonic stem cell (hESC) lines and their differentiated progeny and to monitor feeder contaminations, we have examined gene expression in seven hESC lines and human fibroblast feeder cells using Illumina® bead arrays that contain probes for 24,131 transcript probes. Results A total of 48 different samples (including duplicates) grown in multiple laboratories under different conditions were analyzed and pairwise comparisons were performed in all groups. Hierarchical clustering showed that blinded duplicates were correctly identified as the closest related samples. hESC lines clustered together irrespective of the laboratory in which they were maintained. hESCs could be readily distinguished from embryoid bodies (EB) differentiated from them and the karyotypically abnormal hESC line BG01V. The embryonal carcinoma (EC) line NTera2 is a useful model for evaluating characteristics of hESCs. Expression of subsets of individual genes was validated by comparing with published databases, MPSS (Massively Parallel Signature Sequencing) libraries, and parallel analysis by microarray and RT-PCR. Conclusion we show that Illumina's bead array platform is a reliable, reproducible and robust method for developing base global profiles of cells and identifying similarities and differences in large number of samples. |
| Databáze: | OpenAIRE |
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