Genes that are up- or down-regulated during differentiation of human embryonic stem cells

A method for assessing a culture of undifferentiated primate pluripotent stem (pPS) cells or their progeny, comprising detecting or measuring:

• a marker from the following list:
• Cripto, gastrin-releasing peptide (GRP) receptor, and podocalyxin-like protein;
• and
• either hTERT and/or Oct 3/4, or a second marker from the list.

A method for maintaining pPS cells in a pluripotent state, comprising causing them to express one of the following markers at a higher level:

• Forkhead box O1A (FOXO1A);
• Zic family member 3 (ZIC3);
• Hypothetical protein FLJ20582;
• Forkhead box H1 (FOXH1);
• Zinc finger protein, Hsal2;
• KRAB-zinc finger protein SZF1-1;
• or Zinc finger protein of cerebellum ZIC2;
• or
• any other marker listed in Table 5 with the symbol “{circle over (x)}”.

A method for causing pPS cells to differentiate into a particular tissue type, comprising causing them to express one of the following markers at a lower level:

• Forkhead box O1A (FOX01A);
• Zic family member 3 (ZIC3);
• Hypothetical protein FLJ20582;
• Forkhead box H1 (FOXH1);
• Zinc finger protein, Hsal2;
• KRAB-zinc finger protein SZF1-1;
• or Zinc finger protein of cerebellum ZIC2;
• or
• any other maker listed in Table 5 with the symbol “{circle over (x)}”;
• or by causing them to express one of the markers listed in Table 6 with the symbol “{circle over (x)}” at a higher level.

A method for identifying genes that are up- or down-regulated during differentiation of pPS cells, comprising:

• a) sequencing transcripts in an expression library from undifferentiated pPS cells;
• b) sequencing transcripts in one or more expression libraries from one or more cell types that have differentiated from the same line of pPS cells;
• c) determining the frequency of transcripts from each gene sequenced in each of the libraries;
• and
• d) identifying the gene as being up- or down-regulated during differentiation of the pPS cells if the frequency of transcripts in the library from the undifferentiated pPS cells is statistically different from the frequency of transcripts in one or more libraries from the differentiated cell types.