The TruSeq DNA/RNA, old PE (Paired-End) Genomic DNA, Nextera, and old Paired-End Multiplexing adapters work on all Illumina platforms and can be read as a single read or paired read. TruSeq small RNA adapters will work on all platforms, but can only be used for a single forward read.
The OLD small RNA adapters work only for a forward read on Single Read flowcells on the HiSeq2000 or GA, which are no longer in use. We strongly recommend you do not use them to build new libraries.
If you use Illumina adapters with indexes built in, you must let us know and request a multiplex read when you submit your samples. This is an additional priming and sequencing read and will cost extra.
See the FAQ about indexes vs barcodes if you are interested in doing the barcoding "inline" within the main fragment read.