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.
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.


CONCLUSIONS
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.
Liu
Ying
Y
Laboratory of Neurosciences, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, Maryland 21224, USA. yliu21224@yahoo.com
Shin
Soojung
S
Zeng
Xianmin
X
Zhan
Ming
M
Gonzalez
Rodolfo
R
Mueller
Franz-Josef
FJ
Schwartz
Catherine M
CM
Xue
Haipeng
H
Li
Huai
H
Baker
Shawn C
SC
Chudin
Eugene
E
Barker
David L
DL
McDaniel
Timothy K
TK
Oeser
Steffen
S
Loring
Jeanne F
JF
Mattson
Mark P
MP
Rao
Mahendra S
MS