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English: Genome-wide expression profiling using expressed sequence tag (EST) analysis, serial analysis of gene expression (SAGE), DNA microarrays and massively parallel signature sequencing (MPSS) have all been used to study the transcriptome of ES cells. ESTs are generated by inserting cDNA into cloning vectors to produce a cDNA library. The inserts are sequenced and the resulting EST sequences are analyzed. SAGE involves the generation of gene-specific tags, typically 10–14 basepairs in length. These tags are ligated to form di-tags, amplified by PCR, ligated again to form concatamers and sequenced. Expression microarrays are arrays of synthesized oligonucleotides or spotted cDNAs in a predetermined spatial orientation. Total RNA is reverse transcribed, fluorescently labeled and hybridized to the microarray. Specific hybridization signals are detected by a fluorescent scanner, and gene expression is deduced. Tiling arrays are modified microarrays where all non-repetitive genomic DNA is represented at various sequence resolutions. Unlike conventional microarrays, tiling arrays enable the discovery of novel transcribed sequences and regulatory elements through the unbiased examination of the genome. MPSS involves the cloning of a cDNA library on beads and the acquisition of 17–20-nucleotide tags from these cDNAs using an unconventional sequencing method that allows for large-scale sequencing. Recently developed deep sequencing approaches using 454 and Solexa platforms promise to provide a comprehensive description of the pluripotent transcriptome.