Flow cells of the high-output-mode of the Hiseq 2500 instrument are physically subdivided into 8 channels. In 1 channel up to 180 million clusters can be sequenced from one or from both ends.
Given this huge data output, we often recommend pooling of several samples in one channel in order to save sequencing costs. Here we use molecular barcodes (stretches of specific nucleotides) to tag up to 12 unique samples in a single channel. This is appropriate for most applications, like mRNA sequencing or ChIP sequencing.