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Human embryonic stem cells(hESCs),derived from the inner cell mass of human blastocysts,are considered to be the most pluripotent of all stem cells.Both feeder-dependent and feeder-free culture systems are applied to maintain self-renewal hESCs.However,hESCs of different culture systems showed different morphology,there might be different transcriptional and functional differences between these hESCs.To test this hypothesis,we first derived three hESCs lines under the culture system of human foreskin fibroblasts (HFF) combined with mTESR1,and the stem cell characteristics were identified.And then,we conducted a large-scale transcriptional profiling of IncRNAs and mRNAs in these three pairs of hESCs cultured under feeder-dependent and feeder-free culture systems using microarray technology.